 Introduction History and geographical location of the unit

The UMR DGIMI was created in January 2011 by merging two UMRs: "Microbial Ecology of Insects & Interactions Host-Pathogens" (EMIP) and "Integrative Biology & Virology of Insects" (BIVI). The UMR EMIP moved from Saint-Christol-les-Alès to the Université Montpellier 2 (UM2) Campus in 2001 and the UMR BIVI in 2005. As a consequence, the team "Proteomic study of the interaction Spodoptera-microorganisms" was merged with the team "Biological resources & genetic of bacteria and entomopathogenic nematodes" in 2011. In 2013, this new team was merged with the team "Functional genomics & virulence factors" to constitute the current team "Integrative biology of bacteria-insects-entomopathogenic nematodes interactions" (BIBINE).

All members of the UMR DGIMI are now located on the Triolet Campus of UM2 (3rd and 4th floor,building 24), in Montpellier. The insectarium is located within the same Campus (building 55, Center for animal facilities).

The UMR DGIMI belongs to the "Plant Health & Environment" (SPE) Department of Inra and the "Environment, Lifesciences, AgriFood, Planetology" (EVAP) Department of UM2 (Section "Integrative biology, Plants, Interactions").

Management team

The current direction: Mr Patrick TAILLIEZ (director) and Ms Anne-Nathalie VOLKOFF (deputy-director)

The project leaders/future direction: Ms Anne-Nathalie VOLKOFF (director) and Mr Alain GIVAUDAN (deputydirector).

AERES nomenclature

Domaine disciplinaire principal: SVE1_LS6Immunologie, microbiologie, virologie, parasitologie Domaine disciplinaire secondaire 1: SVE1_LS2 Génétique, génomique, bioinformatique Domaine disciplinaire secondaire 2: SVE_LS9 Biotechnologies, sciences environnementales, biologie synthétique, agronomie

Unit workforce

Unit workforce

Doctoral students 5

Theses defended 8

Postdoctoral students having spent at least 12 months in the unit* 9

Number of Research Supervisor Qualifications (HDR) taken 3

Qualified research supervisors (with an HDR) or similar positions 9 7

2  Overall assessment of the interdisciplinary unit

Global assessment of the unit

The overall assessment of the unit is excellent. In the socio-economic context of insect pest control and the necessity to propose biological alternatives to chemical insecticides, the unit DGIMI develops an original integrative approach (from molecules to organisms) in order to study the molecular mechanisms of the interaction between plants, Lepidoptera, pathogens and parasites (densovirus, nematodes and nematode-associated bacteria, hymenoptera and hymenoptera-associated viruses). The scientific production between 2008 and 2013 involves 54 papers (ACL), most of them being published in high standard journals. One major deliverable of their research activity is the contribution to three databases: I) a comparative genomics database on Lepidoptera pests of crops and their parasitoids (LepidoDB); II) a database on Spodoptera EST; III) a database on genome analysis of Photorhabdus and Xenorhabdus.

The unit is well funded by regional and national programs (six ANR projects, two projects as coordinator), and has strong links with two private companies (this includes the presence of four people from one company hosted in the unit, and a phase 2 product with the second one). The unit members are involved in training at both the License and Master level. In particular, they coordinate one Master specialty. The number of PhD sudents (8 theses defended and 5 in progress) should be increased in the future. Based on the meeting with the members of the unit (researchers-lecturers, engineers, technicians, administratives and students), the general feeling on the unit life and the scientific activities is excellent.

Strengths and opportunities related to the context

• they manage a complete range of pathogens and parasites associated with crop-infesting Lepidoptera;

• they share common tools and methods to study the various partners (e.g., genomics);

• they share live material resources such as the Insect rearing facility (Insectarium), the Platform for experiments on Quarantine Insects (PIQ), three collections (nematodes, bacteria, insect cell lines), and tools for functional genomics;

• they have a very good level of economic interactions especially with two private companies;

• they are heavily involved in microbiology and parasitology teaching and networking (co-creation of a "Interaction Microorganism-Host" (IMH) network with the LSTM unit);

• according to previous recommendations, they increased their collaboration with the CBGP unit allowing studies at the population level.

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Weaknesses and threats related to the context • the number of PhD students in average is quite low and can be easily increased;

• the absence of EU funding during the last period;

• the age pyramid is not favorable and will require recruitment or attraction of young researchers/lecturers and technicians/engineers in the near future;

• the teams have to adjust their objectives to their size (in terms of number of permanent positions) and strengths. On the other hand, the size should be increased by hosting more PhD students.

Recommendations

• the members of the unit are encouraged to continue their efforts in building infrastructure in research and education and microbiology/parasitology networks at the regional scale. The animation of the IMH network and the construction of a SFR dedicated to "Invertebrates/environment" are particularly encouraged;

• they have to increase their international recognition through the coordination of larger international projects (EU projects/H2020 on biocontrol), the participation to international conferences as invited speakers, and publication in more generalist journals with high impact factor;

• they have to set research priorities both at the team and unit level that are appropriate with the size, strengths and skills of the teams/unit;

• they are encouraged to make the unit more attractive for PhD students and diversifying the origin of the PhD grants (e.g., CIFRE);

• associate-professors are encouraged to defend their HDR whenever possible;

• the teams are encouraged to increase collaborations between them through common projects;

• they are encouraged to, at the very least, maintain the current level of interactions with private companies.

 Detailed assessments

Assessment of scientific quality and outputs

The overall scientific production of DGIMI members between 2008 and 2013 is excellent, with 54 papers (ACL) published, many of them in high impact journals. The mean number of citations per paper is 9. The journals in which they published their results includes 'generalist' journals (Science, PNAS, PLoS One) and 'specialized' journals (BMC Genomics, Gene, Int J Syst Evol Microbiol, Insect Biochem Mol Biol, J Insect Physiol, J Invert Pathol, Environ Microbiol, J Virol, Mol Immunol). The average number of papers per permanent researcher/lecturer and per year is 0.8. Several members of the unit are co-authors of five patents in total.

Taking into account the quality of the research and its international positioning, the level of publications, especially in term of targeted 'generalist' journals with a high impact factor, could be easily increased.

Among the major results with high impact the experts committee would like to highlight the following:

• the role of holocentrism on evolution rates in Leptidoptera (PNAS in 2010, cited 40 times) and the characterization of the holocentric structure (PLoS One in 2011). One important result is the evidence that holocentric chromosomes allow faster evolutionary rates compared to monocentric ones;

• baculoviruses were shown to derive from the integration of a nudivirus in the genome of a braconid ancestor (Science in 2009, cited 94 times).Within the Hyposoter didymator genome, regions specialized in the production of proteins associated with IVs particles were shown to be amplified during viral replication (PLoS Pathogens in 2010, cited 36 times);

• the characterization of regulatory networks controlling pathogenicity in Xenorhabdus, involving the examination of fliZ expression at the single cell level (PLoS Genetics in 2013);

• a major contribution to the understanding of densovirus infection and replication (three papers published in J Virol).

Another important deliverable of their research activity is their involvement in the elaboration of three databases hosting genomic resources: I) a database on comparative genomics dedicated to Lepidoptera pests of crops and their parasitoids (LepidoDB), in collaboration with the BIPAA platform in Rennes; II) a database of Spodoptera EST created in 2006; III) a database on genome analysis of Photorhabdus and Xenorhabdus (PhotoScope & XenorhabduScope) in collaboration with the Genoscope (CEA, Evry) and the 'Xenorhabdus US Consortium'.

They collectively manage a collection of living entomopathogenic nematodes (about 210 strains), a collection of their symbiotic bacteria (about 440 strains), and a collection of densovirus.

Assessment of the unit's academic reputation and appeal

The overall assessment of the academic reputation and attractiveness of the unit is very good. Several members of the unit contributed to the leadership in Lepidoptera genomics through the coordination of the Spodoptera sequencing project and the ADALEP (Adaptation of Lepidoptera to biotic environment) network. They also participated to the Fall ArmyWorm International Public Consortium (FAW-IPC) for the annotation of Spodoptera frugiperda genome and the 'Bombyx Genome Consortium'. They are members of the 'International Consortium on Xenorhabdus Genomic'.

They participated to the organization of two national meetings (ImmunoInv 2008 andEntomo 2012 in Montpellier) as members of the Scientific Council. Several members of the unit were invited to ten international meetings in total.

They coordinated two Franco-Libanese projects (CEDRE 2007(CEDRE -09, 2009-10-10) and a project with Brazil (CAPES-COFECUB, 2009-10). They have been involved in two projects funded by ANR (Agence Nationale de la Recherche) as coordinator (ANR Blc 'Holocentrism'/2007-11 and 'ADA-SPODO'/2012-15), and four as partner (ANR Blc 'GnpAnnot'/2007-11, ANR Blc 'Paratoxose'/2009-12, ANR Systerra 'Biocosmac'/2009-12, and ANR BioAdapt 'ABC-PaPoGen'/2012-16). Several others projects (7) were funded by national (Inra-SPE, Inra AIP-Bioresources, Genoscope) and regional (UM2) programs, as coordinators or partners.

Their attractiveness can be measured by five invitations of researchers/professors and the welcoming of nine post-docs students. One member of the unit received a 'young lecturer' IUF grant (Institut Universitaire de France).

Assessment of the unit's interaction with the social, economic and cultural environment

The interaction with the economic environment is very good. They have a strong link with two private companies: four people from the 'In Vivo Bioresources' company (two engineers and two technicians) are hosted in the unit to carry out programs on biological control of crop pests in collaboration with the DIDI team. The collaboration between the BIBINE team and the Nosopharm company on new antibiotics resulted in patents with license and a phase 2 product.

Assessment of the unit's organisation and life

The organization and the life of the unit was evaluated as excellent. The organization of the unit is now stabilized with four research teams (EHA 'Epigenetic, Holocentrism & Adaptation', BIBINE 'Integrative Biology of Interactions Bacteria-Insects-Entomopathogenic Nematodes', DIDI 'Dynamics of Interactions of Densovirus-Insects' and B2iHP 'Integrative Biology of Host-Parasitoid Interactions'). They share live material resources such as the Insect rearing facility (Insectarium), the Platform for experiments on Quarantine Insects (PIQ), three collections (nematodes, bacteria, insect cell lines), and tools for functional genomics.

The quality of the unit's organization and life relies on the collegiality of the decisions at the unit level including researchers/lecturers, engineers, technicians and support staff, the frequent and regular meetings involving all the members (permanent positions) of the unit, and the organization of regular scientific seminars.

The meetings between the experts committee and the different groups of the unit confirm the very positive general feeling of the experts committee on the unit's management and life.

Three levels of decision taking exist: the Scientific Advisory Board involves the unit's direction and team leaders (about six meetings per year); the Lab Council (life organization of the unit) involves all unit members (three-four meetings per year); working groups dealing with Insectarium, Platform of Insect Quarantine (PIQ), Health/Safety/Quality.

Assessment of the unit's involvement in training through research

They have a very important contribution in education at the Master level, including the coordination of the Master specialities (Section BioPMBB 'Plant and Microbial Biology-Biotechnology-Bioprocess'/Speciality IMHE 'Interactions Microbes-Hosts and Environment', Section EcoBioDiv 'Ecology-Biodiversity'/Speciality IEGB 'Engineering in Ecology and Biodiversity Management' at UM2, and Section BSE 'Biology-Health-Ecology'/Speciality SSIB 'Signalisation-Integrated Systems in Biology' at EPHE).

Two members of the unit contribute to the life of their Doctoral School (ED n°477 SIBAGHE, 'Integrated Systems in Biology, Agronomy, Geosciences, Hydrosciences, Environment') through the coordination of the 'Microbiology/Parasitology' Section and the participation to PhD committees as ED SIBAGHE representatives. They published two educational books for students (License, Master).

The number of PhD students (8 theses defended, and 5 in progress) should be increased in the future. All the PhD students (even a few master students) are associated to publications, confirming the good quality of student guidance.

The discussion with the deputy-director of ED SIBAGHE confirmed the important involvement of lecturers and researchers in the ED SIBAGHE functioning, and the quality in training of students through research.

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Assessment of the strategy and the five-year plan Their five-year plan is very ambitious with the following original questions:

• expected breakthrough on the evolutionary of Ichnovirus and mechanisms underlying the success of parasitoid wasps attacking Lepidoptera species of economic relevance;

• genome scale analysis on the major moth pest S. frugiperda;

• population genomics and epigenomics (S. frugiperda) to identify mechanism of adaptation to plants;

• single cell approach to understand bacterial (Xenorhabdus)-host interaction;

• expanding research topics to include evolutionary and ecological aspects of densovirus in order to develop new tools for pest control.

The assessment of the strategy and the project was evaluated as excellent because of the real possibility to increase the interactions between teams due to the very good integration of biological models and approaches. The feasibilty of the five-year plan is reinforced by a more intense collaboration with population geneticists of CBGP (Centre de Biologie et de Gestion des Populations, Montpellier) allowing integrative studies from molecules to populations.

Future associations with geographically and scientifically closely related research units could be the result of joint projects and publications, facilitated by the existing IMH 'Microbial-Hosts Interaction' network and the SFR (Structure Fédérative de Recherche) network 'Invertebrates/Environment' in preparation. 10 4  Team-by-team analysis The main theme of EHA team is to describe the holocentric struture of the genomes of lepidoptera and its implications for functional organization, regulation and evolution of the genome. These questions are addressed on the noctuid Spodoptera frugiderda, on which the team has accumulated genomic ressources (EST, RNAseq, BAC libraries), including a full sequenced genome, through an international consortium.

A search of centromeric proteins pointed the absence of some of them in S. frugiperda and the importance of Transposable Elements (TE) in the evolution of histone-like gene. Search for epigenetic marks in 1 % of the S. frugiperda genome showed that heterochromatine is associated with gene-poor, repeat-rich regions. Transcriptomic analysis of developmental stages of S. frugiperda allowed identifying genes involved in moth development, some of which being validated with siRNA experiments. One important result of the team is an evidence that holocentric chromosomes allow faster evolutionary rates compared to monocentric ones. Finally, the team is developing a project to identify genomic regions involved in plant adaptation in S. frugiperda by comparing genomes of the corn and rice specialized strains.

It is not always clear to understand the influence of holocentrism on genome and epigenome regulation and evolution, in terms of expectations and hypothesis-testing experiments. Although holocentrism is a unifying link of the team, some important issues addressed by the team are not very well connected to this central question.

For a small team like EHA, the production is excellent, both quantitatively and qualitatively, and diversified. Five papers, among which one in PNAS, two patents, and the building of LepidoDB, a dedicated database for lepidoptera of economic importantce and their parasitoids.

Assessment of the team's academic reputation and appeal

The team is very active and recognized in the field of Lepidoptera genomics. This has led to gathering many genomic resources on S. frugiperda and to propose the complete genome sequencing of this noctuid through an international consortium and supports from INRA and Genoscope. This team benefits from internal expertise in bioinformatics (two IE) and from supports from INRA platforms (PF Bipaa in Rennes and URGI in Evry). The team has also coordinated two ANR projects, one running till 2015.

The team also coordinates the French network ADALEP, supported by INRA SPE, and organized last year an international workshop on Lepidoptera genomics and adaptation. It also participates actively to the Bombyx Genome consortium.

The team has recruited in september 2011 an associate professor who is granted by IUF (Institut Universitaire de France) till 2018.

The team publishes in good to excellent journals (e.g. PNAS). The production is excellent and could be improved both quantitatively and qualitatively to make visible the efforts put on the acquisition of genomic resources. The team may increase its scientific recognition through invited participations to national or international symposia. The team has a relatively low number of PhD students (2) and post-doctoral fellowships (1).

The team has fully responded to the request of the Inra SPE division to interact more with the CBGP on population ecology, evolution and genomics of Lepidoptera. The EHA is a partner of an ANR project coordinated by CBGP (Adaptome), is co-supervising two PhD theses with CBGP, and hosts one researcher from CBGP to increase the links between functional and population genomics.

Assessment of the team's interaction with the social, economic and cultural environment

The team develops in collaboration with bioinformatic platforms dedicated databases to gather and publically access genomic resources of Lepidoptera (LepidoDB) and Spodoptera (SpodoBase).

The team has developed patents to silence Spodoptera genes through siRNA delivery. Private partnership is ongoing but it is unclear how it is formalized.

Assessment of the team's involvement in training through research

The team has a rather low activity of training through research (two PhD theses in progress). There is no self-analysis of the team to explain how this could be improved. The fact that the EHA team includes an associated professor (recruited in 2011) should be considered as an opportunity to attract more students on EHA research topics.

Assessment of the strategy and the five-year plan

The project of the EHA team for the next 5 years is on the continuation of what has been done so far. It is still based on holocentrism in Lepidoptera and how this peculiar chromosome structure affects genome organization, functioning and evolution. Two changes are highlighted: I) address these issues at a whole genome scale, taking advantage of the full genome sequence of S. frugiperda; II) reinforce population genomics and epigenomics to identify the mechanisms of plant adaptation in the noctuid, taking advantage of the sequencing of the rice strain and the collaboration set up with CBGP.

The team should make clearer priorities on their scientific orientations, in relation with the actual human strengths of the team (two permanent people left or will leave soon). Interactions with other teams of DGIMI, with CBGP and other INRA teams working on insect genomics should be intensified to enhance research dynamics and overcome critical size effects.

Conclusion

 Strengths and opportunities:

The team has an excellent recognition in the field of Lepidoptera genomics, through consortium initiatives, coordination of a network, development of dedicated databases and recent collaboration with CGBP. The use and valorization of genomic data obtained in Spodoptera are opportunities to better define further orientations and increase team reputation through publications in high ranked journals.

 Weaknesses and threats:

The team must be reinforced. The scientific strategy of the team should be better defined by making priorities, identifying essential needs and exploring important partnerships. There is a possible threat that the team could not reach their 5 year plan objectives mentioned in the document, because of insufficient resources and brainstorming on team priorities sized on actual strength and expertise.

 Recommendations:

The team should continue to lead projects on Lepidoptera genomics but needs to make clearer priorities, based on promising scientific issues, strategic aspects, human resources and expertise in presence. The team should continue and even reinforce collaborations with CBGP and other teams working in insect genomics. The team should also have more internal links within the unit and attract more PhD students and post-docs.

Team 2:

Integrative biology of interactions between bacteria, insects and entomopathogenic nematodes Name of team leader: Mr Alain GIVAUDAN The BIBINE team has resulted from the merger of three teams (the first merger in 2011 and a subsequent merger in 2013) and the team now has 16 permanent members of staff (11 supported by Inra and 5 supported by the Université Montpellier 2). This team has an excellent research output with 38 papers and three patents since 2008. Many of the papers are in excellent journals with high impact factors (i.e. five papers in PLoS One, three papers in Environmental Microbiology, two papers in BMC Genomics, one paper each in Molecular Microbiology, Infection and Immunity, Applied and Environmental Microbiology, CurrOpinMicrobiol, Genome and Journal of Bacteriology, and most recently a paper in PLoS Genetics). This represents a consistently high output for a laboratory in the area of molecular microbiology. In particular the latest research (just published in PLoS Genetics), involving the examination of fliZ expression at the single-cell level, is very exciting and offers this team an opportunity to become researchleaders in the area of population heterogeneity. This team is internationally recognized as being leading experts in the field of Photorhabdus and Xenorhabdus research. They have led the field in their work on the genomics of these bacteria since the publication of the Photorhabdus luminescens TTO1 genome in 2003. Importantly their contribution to the MaGE genomic analysis platform has led to the development of an extremely important resource for the field. Moreover since 2008 the papers published by this team have accumulated a h-index of 8 (calculated from 33 papers that were identified using the three researchers of the team as search terms in Web of Science) and their papers have been cited 172 times, suggesting that their work is having a significant impact in their research area.

Workforce

Three members of the team have been invited to participate in a number of national conferences and some international conferences.

Finally it was interesting to see the protocol to help in the identification of Photorhabdus asymbiotica infections in humans.

Assessment of the team's academic reputation and appeal

This team has an excellent reputation amongst their peers for performing (and publishing) excellent research. The team has secured five grants since 2008 primarily from the INRA SPE department. As outlined in the report, they have also participated in a number of national and international projects/networks ranging from an international Xenorhabdus consortium and a local regional network called "Interactions Micro-organisms-Hosts" (IMH). Their level of participation has ranged from collaborator to organiser. The team has been very active in regional and national networks in particular.

Much of the international work of this team has been with the characterization of nematode-bacteria complexes that have been isolated from around the world. This obviously speaks highly of the reputation of the team as experts in this area. The team has also collaborated with international groups (particularly in the USA) for the sequencing of Xenorhabdus strains. The team has hosted several short-term visits by foreign researchers and one French post-doctoral fellow since 2008. The post-doc has since been recruited by the INRA and is based in Clermont-Ferrand. Members of the team have also acted as ad hoc reviewers for a number of leading international journals and important funding agencies.

Assessment of the team's interaction with the social, economic and cultural environment

The team has partnered with a small start-up company (Nosopharm) since 2009 and this partnership has resulted in three patents in 2012-2013 and a publication in the Journal of Antibiotics in 2013. The patents are protecting specific bioactive molecules (potential novel antimicrobials) produced by the genus Xenorhabdus. There has been much interest, particularly over the last few years, in Xenorhabdus and Photorhabdus as sources for novel antimicrobials and this team is well-placed to take advantage of this interest with their extensive strain collection (> 400 isolates) of Xenorhabdus and Photorhabdus. One of these compounds, NOSO-95, has been shown to be a first-in-class antibacterial molecule active against a number of antibiotic-resistant Gram negative bacteria and this compound is being developed by Nosopharm. The link-up between this team and Nosopharm does appear to be working well with both partners contributing to the interaction (i.e., BIBINE team brings bacterial strains and microbiology skills, Nosopharm brings path to market). Moreover Nospharm and its academic partners have been successful in leveraging money from the French government for the development of NOSO-95, highlighting the potential for this partnership. Several press releases have also been linked to this partnership and there has been widespread on-line advertisement.

Assessment of the team's involvement in training through research

Members of the team have been involved in the supervision of five PhD students that have graduated since 2008. Currently the team is supervising two PhD students. They have supervised nine Masters students (Master 1 and 2). Therefore this team has made a significant contribution to training through research in this unit.

Staff members are also involved in the running of post-graduate Masters programs and members of the team were critically involved in the development of new Masters course in "Integrative Parasitology".

Assessment of the strategy and the five-year plan

The BIBINE team is proposing to develop their work on the analysis of single-cell gene expression in bacterial populations. They appear to be well-placed to do this (with an excellent recent publication in PLoS Genetics) and this is going to be a very exciting new field of research in bacteriology. This work will be used to develop a better understanding of the roles of phenotypically distinct sub-populations of Xenorhabdus during the tripartite interaction. In addition the team proposes to study the nematode microbiome to determine the effect of other bacteria on the nematode-Xenorhabdus interaction. This is in line with an increased interest in studying how entomopathogenic nematodes and their symbiotic bacteria compete with the normal microbiota of their hosts.

Conclusion

 Strengths and opportunities:

The team is composed of excellent researchers with a lot of experience in molecular microbiology. This experience will ensure rapid progress towards the objectives of the proposed project. The team is also well placed because of its access to the PIQ platform and its existing collaborations with other teams in the unit. These collaborations must also be seen as an opportunity and efforts to develop these links should be encouraged. Finally, the existing collaboration with Nosopharm is very exciting. In this collaboration the team has provided Nospharm with access to their extensive Xenorhabdus strain collection. This collaboration must also be used as an opportunity to leverage more funding for the team from sources such as the EU.

 Weaknesses and threats:

The team is currently quite big and dynamic but it is imperative that new, young researchers are attracted to join it to ensure continuity. Moreover, the range of current funding sources are very limited and the team is encouraged to increase the diversity of funding sources to prevent any sudden changes in available funding.

 Recommendations:

The team is encouraged to exploit opportunities within Horizon 2020, including Marie-Curie fellowships, ERC fellowships (particularly early-stage and/or consolidator fellowships). The team have access to a number of resources that should attract potential EU-based collaborators (i.e. PIQ platform, strain collection). This would strengthen the funding base and also increase the profile of the team across Europe. The team is also encouraged to participate in more international conferences. This will increase their visibility and awareness of the exciting resources that they can access. During the last years, this team has made a major contribution to the understanding of the biology of densoviruses, using Junonia coenia densovirus (JcDNV) as a model. In that sense, the team has specially contributed to the understanding of the molecular mechanisms involved in the viral entrance, replication and systemic spread in the host. The excellent quality of such research is reflected by the publication records. Different aspects of JcDNV pathology and specificity have been published in top journals in the area of virology (J. Virol and Virol).

The team has also focused, more recently, on the study of densovirus evolution and ecology. Nevertheless, the team has made certain contributions that could have a major impact on that topic in the near future. Among such contribution, it is remarkable the discovery of changes in host behavior after viral infection and the development of methodologies for the finding of novel densoviruses in the field infecting new species of agronomical importance. Such results are not published yet, although, according to the report, several manuscripts covering such aspects are in preparation.

Assessment of the team's academic reputation and appeal

The team reputation is reflected in its interaction with other research groups (Mr Morena CASARTELLI, University of Milan, Italy; Mr Yi LI, Wuhan University, China; Ms Keiko KADONO-OKUDA, NIAS Tsukuba, Japan) working on related topics. Moreover, their studies have been published in top virology journals.

Recent and future studies on understanding densovirus evolution and ecology have increased their interdisciplinary from a conceptual as well as methodological point of view. It has been mainly realized by the establishment of national collaborations and consortiums (BGPI, Montpellier; INRA Bordeaux; INRA Avignon). It is expected that such collaborations will increase group reputation at the same time that will promote international visibility.

Assessment of the team's interaction with the social, economic and cultural environment Research conducted by the team has allowed the transfer of knowledge to a company for the development of novel agents for pest control. This gives an added value to the research with a possible substantial contribution to the economic developed of the region/country in the context of the "knowledge economy".

Additional collaborations on the development of densoviruses as a delivery vector, although still very premature, could also contribute in a long term to the economy of the region.

Assessment of the team's involvement in training through research

According to current and future plans, the team is broadening its research topic to evolutionary and ecological aspects of densoviruses, creating a more multidisciplinary environment. Such type of environment is especially attractive for national and international students and researchers, and has a major impact of the training capacity of the group.

Assessment of the strategy and the five-year plan

Future plans are mainly focused on completing or getting more information on molecular and cellular aspects of the pathological process of densovirus infection as well as getting more information on ecological aspects. This should contribute to a better understanding of the pathological process occurring in the field and subsequently to the development of effective agents of pest control.

Having good connections with companies on the field, it would be interesting to focus on more applied aspects of densoviruses. For instance, very few aspects of the densovirus interactions with other biological control agents (parasitoids, predators and microbial control) being already in use for pest control are considered in the future plans. Knowing practical aspects of the interaction would strongly contribute to the development, alone or in combination, of densovirus as a biological control agent.

Conclusion  Strengths and opportunities:

Densoviruses are restricted to arthropods and as a final outcome produce the death of the host, making them very attractive as biological control agents. The knowledge generated by the group on the viral pathology and ecology will be essential to allow a proper use of these virus insuring a safe transfer from the bench to the field.

 Weaknesses and threats:

According to previous comments, research should not only focus on the development of basic knowledge but should also take the advantage of the collaboration with companies to focus on more applied issues.

They should increase international cooperation and funding, especially through the use of EU-instruments.

 Recommendations:

Recommendations are related to the above mentioned weaknesses. The team should give more value to the applied research and that could be mediated through the cooperation projects involving companies working on pest control and using, if possible, EU instruments. The B2iHP team conducts its research on insect parasitoids and is interested on the molecular mechanisms between the endoparasitic wasps and their insect hosts. Basically, two main fields are investigated to learn more about the parasitism success, including the identification and molecular characterization of maternal virulence factors mainly on the ichneumonid Hyposoter didymator, and studying their evolutive origin through different groups of hymenopterans and in collaboration with CNRS national groups. Only few national and international teams are developing this research because of the difficulty to access these non-conventional systems. B2iHP team uses comparative and functional genomics approach to identify candidate genes and to study their function and their impact on the physiology of the lepidopteran hosts. When possible, this team has evolved emerging technologies and concepts, such as the use of sncRNA as possible regulatory elements, and has tackled original questions. The scientific production is excellent (12 papers including one PloS Pathogens and one Science), taking into account the model difficulties and the number of people being involved. B2iHP has a solid national collaboration and reputation while it should strengthen international interactions.

Assessment of the unit's academic reputation and appeal

The B2iHP team is very dynamic both at the national and the international levels, although it should pay more attention to increase its international influence. It has been involved in the organization of two national meetings (ImmunInv08, Entomo12) and is currently working on a REID (Réseau Ecologie des Interactions Durables) network workshop. B2iHP team has also been involved on three ANR projects as a partner, several Inra SPE projects leaded by the team researchers, and other projects supported by the national Genoscope and the Université Montpellier 2. The team leader has chaired one CAPES/COFECUB project. The team has hosted four post-doc students and supervised one PhD student. Scientific expertise was mainly devoted to review papers and to participate to PhD and HDR evaluation committees. The team leader is also involved in many local, INRA, and national tasks, including the scientific council of the SPE department and the steering committee of the structuring issue "Biological Control".

Assessment of the team's interaction with the social, economic and cultural environment

The research questions investigated by the B2iHP are academic but target a social and economic issue that is the identification of new methods and potential bio-pesticides to control insects damaging crops. The final objective through the understanding of parasitism efficiency is to select parasitoid traits and strains having detrimental impacts on the lepidopteran pests that cause huge damage on crops. The team members have actively contributed to development of a database for Spodoptera and the team leader has contributed to the dissemination of knowledge for educational purposes. Science dissemination and vulgarization is also made through book chapter publication and meetings.

Assessment of the team's involvement in training through research

The team has supervised four post-doctoral students and one PhD student. They also have welcomed a pre-doc student from Brazil. The team leader has participated to the organization of two national meetings, ImmunInv 2008 and Entomo2012 as the coordinator of the scientific committee.

Assessment of the strategy and the five-year plan

The five-year project will be focused on H. didymator to deeply understand how HdIV encoded proteins impact the Lepidopteran physiology by characterizing host pathways related to immunity and metabolism and to identify elements interfering with these functions. Genes of interest will be further explored with functional studies and extended phenotypes will be checked and characterized. At the evolutionary point of view, the team has previously demonstrated that two viral acquisition events have occurred within the Campopleginae. They aim now to further characterize the evolutionary history of virus acquisition within the ichneumonid wasps and to decipher the molecular nature of virus particles within this insect subfamily. Ecologically, B2iHP team intends to uncover how genetic variability of the H. didymator virus is correlated with the level of virulence and to identify genes involved in the fitness/virulence traits. While this project is in continuity with the previous one, it will help exploring the genomic and the transcriptomic data accumulated during the previous contract both at the mechanistic and the ecological levels.

Conclusion

 Strengths and opportunities:

• high rank of academic publication including one PLoS Pathogens and one Science paper in collaboration with a team from the Université de Tours;

• good involvement on national congress organization;

• good implication in national thesis, HDR and hiring committees;

• highly dynamic in national collaborations through ANR projects, sequencing projects, INRA projects, national networks, and consortia;

• local responsibility on insect resources and platforms.

N6

  Epigenetics, holocentrism and adaptation of the insectName of team leader: Ms Emmanuelle D'ALENÇON Workforce Permanent EPST or EPIC researchers and similar positions 1,6 1 N3: Other permanent staff (without research duties) 2,2 1,9 N4: Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors, etc.) 1 spent at least 12 months in the team 1 Number of Research Supervisor Qualifications (HDR) taken 1 Qualified research supervisors (with an HDR) or similar positions 1,6 1  Detailed assessments Assessment of scientific quality and outputs

N4:

  Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers(DREM, Postdoctoral students, visitors, etc.)

N4:N6

  Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors, etc.) 1

Number as at 30/06/2013 Number as at 01/01/2015

	N1: Permanent professors and similar positions	3,5	4,30
	N2: Permanent researchers from Institutions and similar positions	9,6	8
	N3: Other permanent staff (without research duties)	18,6	16,6
	N4: Other professors (Emeritus Professor, on-contract Professor, etc.)
	N5: Other researchers from Institutions (Emeritus Research Director, Postdoctoral students, visitors, etc.)		2
	N6: Other contractual staff (without research duties)	6
	TOTAL N1 to N6	37,7	30,9

Unit workforce Number as at 30/06/2013 Number as at 01/01/2015

21

 Weaknesses and threats:

• weak involvement on education through research (one PhD student only) and socio-cultural initiatives;

• the team leader has already been invited and has attended several international meetings but should improve international influence through collaborations, international congress attending and organization.

 Recommendations:

The team should focus research on a limited number of models, (ideally one as it is the case in the team project), which will help increasing the efficiency and deciphering the molecular mechanisms that drive parasite virulence:

• strengthening international visibility through the leadership of international projects;

• reinforcing education through research by supervising more PhD/master students, but also by organizing public meetings for science vulgarization;

Now with three researchers (although the team leader will be chairing the lab), the team should increase the amount of papers published in high rank reviews. From 8.45 to 12.15 pm presentation of the unit results (by the head of the UMR), followed by the presentation of results/project of the four teams (by team leaders) and finally presentation of the unit project (by the new head of the UMR).

From 1.30 to 2.00 pm visit of the quarantine insect platform.

From 2.00 to 5.00 pm meeting with the 'researchers, lecturers' group, the 'technicians, engineers, administratives' group, 'PhD students and post-docs' group, the representatives of INRA and UM2, the deputy-director of the ED 'SIBAGHE' and finally the UMR direction (currrent director, next director and deputydirector).

From 5.00 to 8.30 pm meeting of the experts committee, writing of the report.


president  Mr Didier Houssin

Pierre

 Introduction History and geographical location of the unit

The LGDP lab or its ancestor was established in 1966 and has been associated to the CNRS ever since. It is now an UMR between CNRS and UPVD (Université de Perpignan Via Domitia) located in Perpignan. This location next to the large research centers of Barcelona is very favourable for international interactions. Also the proximity to the Plant Biology-oriented research groups of Montpellier is suitable for fruitful cooperation.

Management team

Mr Jean-Marc DERAGON, director. He is assisted by a technical assistant director and technical services also coordinated by a technical assistant. 2  Assessment of the unit

AERES nomenclature

Strengths and opportunities related to the context

The LGDP laboratory is situated in a small University (Perpignan). It is a structure with a staff of nearly 40 permanent members, nearly half of the senior researchers being CNRS employees. It has thus a rather large-size CNRS staff in relation with the relatively small size of the unit. The lab is organized in 5 teams and several shared platforms. The scientific output of LGDP is excellent with a large number of publications in high quality journals. They have done in particular a number of breakthroughs in the fields of genome organization analysis, epigenetics and regulation linked to stress response. The local, national and international networking of the different teams is of high quality as they have collaborated with one another, but also with several top teams in their respective fields. The publications generated are in general extremely well cited and the international recognition of the researchers is high. Their capacity to get grants (particularly ANR) is very good. Funding by CNRS is one of the highest per capita for plant labs, being nearly at the level of UPR (Unité Propre de Recherche) structures. This is clearly recognition of the high quality research performed in Perpignan. The functioning of the lab seems to run smoothly thanks to the efforts of the director and of the team leaders. Of particular importance is the distribution of tasks of the technical staff between groups and platforms which seems to be satisfactory to everybody. Decisions are made collegially and the different categories of staff and students have expressed deep satisfaction concerning their working conditions. The projects of the different research teams have been highly rated, as necessary adjustments have been made to steer research in the right direction. There is every reason to believe that LGDP should be able to continue on the path of excellence, provided public funding does not dry up in the next contract.

Weaknesses and threats related to the context

One weakness that was noted by the committee is that the lab has got only public grants. They do not perform translational research, nor do they plan to do it in the project that has been presented to the committee. It has been argued that, as a CNRS lab, their mission is to do basic research which does not necessarily imply pursuing private contracts. Nevertheless, if future public funding dries up, the financial equilibrium of the structure could be difficult to maintain. This has been discussed between the committee, the team leaders and the director. They are aware of this danger and are still in the process of defining the best opportunities for obtaining grants from the private sector. Another minor threat is the relatively small size of some of the groups (sometimes only two to three permanent staff, the assistant professors being also quite busy with teaching and administrative duties). LGDP has to pay attention to this, especially as there are few colleagues retiring during the next contract and so few opportunities for position replacement. The director and team leaders have indicated on several occasions that the private sector in agroindustry is severely restricted in the Perpignan area and that the high unemployment rate does not help attracting outside colleagues, due to the difficulties in obtaining a job for either husband or spouse. The opportunity to attract a new team leader (and a new team) vs reinforcing present teams has also been debated with the committee.

Recommendations

The committee wishes to indicate first that the project builds on acquired know how and competences of the staff. In general, it is well balanced and achievable. It is expected that there should be no major problem for maintaining high standards of research in LGDP in the next contract as the organization of the lab seems to run smoothly. The involvement of team members in University and CNRS councils is helpful and should be continued. The University (a structure of modest size) and CNRS have pledged their support for this team which is a major player in the narrow biological field of Perpignan, so there is no cause for concern there. The committee advises LGDP to maintain and strengthen its international ties with Catalogne as they are in an ideal geographical position for this purpose. Also the scientific relations with Montpellier should absolutely be maintained. It is also suggested, if possible, to try to obtain private contracts in the future in order to secure a more diverse source of funding. Finally, attention should be paid to maintain the staff in the various research teams at a level sufficient for competing internationally. Attracting more post docs would be desirable to strengthen the lab's international recognition.

3  Detailed assessments

Assessment of scientific quality and outputs

Overall, the scientific production quality of LGDP ranges between very good to outstanding with an "excellent" average. Given the moderate size of the lab, a large number of top quality papers have been produced in high ranking international journals (Nature, Science, PNAS, Plant Cell, Mol Cell, EMBO J etc…). These papers are already well quoted, they include quite often collaborators with high reputation in the field. Nevertheless, on several occasions, LGDP researchers are clearly the leaders of the project. In other words, they have created a network of excellent collaborators but they maintain a very good rank in this network with original contributions where they are leading.

Assessment of the unit's academic reputation and appeal

This has already been discussed in the summary statement and previous paragraph. LGDP has true outstanding international collaborations with top class researchers from Switzerland, USA, Taiwan, Spain, Chile, UK etc… but also with top French researchers. Nevertheless they have difficulties in attracting post-docs in Perpignan, perhaps because of the economic situation in Languedoc Roussillon and neighbouring Catalunya. They have a regular flow of PhD students from the Perpignan Ecole doctorale and also from Labex and ANR grants. Still a higher number of students could be trained, especially in the groups with several CNRS researchers. One indicator of the high LGDP's reputation was the election of one of its members to the French Academy of Sciences, but they also participate to many other French and international committees.

Assessment of the unit's interaction with the social, economic and cultural environment This is possibly the weakest point of LGDP assessed as good with the following comments:

While they are doing much effort in terms of interaction with the social environment (eg unanimous participation of all the groups to the Fête de la Science, welcome of junior high school and primary school students), there is little or no activity to report with the industry, which could become critical in the short future. The researchers and director of LGDP are well aware of this problem and wish to fix it. It is not clear yet what path they will follow to do that. A number of efforts have been made to reach information networks.

Assessment of the unit's organisation and life

This can be clearly considered as a success story. This is due both to the current director's actions and also to a good spirit of collaboration within the board of group leaders. Obviously, LGDP has in the past known some turbulence but those days are apparently over and the organization of the lab can be considered as outstanding.

During the visit all staff categories have expressed satisfaction at the way things were currently run. It was mentioned several times that they function collegially and not top to bottom. The organization of the technical platforms seems also to be a success and the good atmosphere in the lab is reflected by the high proportion of shared grant money. Still they should aim at an IBIZA ranking of their technical facilities.

Assessment of the unit's involvement in training through research

Nearly half of the LGDP staff are teaching at the Bachelor and Master levels. Additionally, they have trained more than 15 PhD students in the last contract. This seems like a reasonable number taking into account the relatively small size of the Perpignan University and École Doctorale (typically they obtain 1-2 PhD grants from the French Ministère de la Recherche et de l'Enseignement Supérieur per year). The number of post docs is relatively modest and should be improved, if possible, in the next contract. Overall, the involvement in teaching through research is very good to excellent.

Assessment of the strategy and the five-year plan

The research project of LGDP was presented team by team. They have taken into account the changes in staff size especially in Teams 1 and 5 and reduced some projects accordingly. All projects are convincing and quite well balanced. They have been rated between very good and outstanding with an average of excellent. These research projects are assessed in details in the following sections of the report and the reader is advised to go through the individual team reports to get a good feel of their diversity and level of excellence. Given the expertise and previous achievements in LGDP it is expected that this lab should be able maintain its level of excellence in research. In this respect, the committee feels the major risks resides of not being able to accomplish the desirable research plan because of the lack of diversification of research funds. Indeed basic science oriented research on model plants may not achieve the required level of funding. Along these lines the committee and unit director have discussed on the possibility of attracting a new team. This possibility is now debated and the relative merits of choosing this solution rather than consolidating the teams which have already a low number of permanent staff are being weighted.

4  Team-by-team analysis Team 1 :

Stress-induced post-transcriptional reprogramming of plant gene expression

Name of team leader: This team is dedicated to the investigation of plant adaptation to stress, and in particular the study of posttranscriptional mechanisms by which plants modulate stress responses. The group largely focuses on Arabidopsis thaliana as its model organism. Its research directions for the previous period can generally be broken down into two sub-themes: the importance of Short INterspersed Elements (SINEs) in plant development and stress adaptation, and the importance of the LA-related proteins (LARPs) in post-transcription gene regulation, and in particular heat shock stress adaptation. The group has published 12 peer-reviewed, PubMed indexed research articles in the past five years, of which six can be attributed primarily to this team, all in journals ranging in quality between strong and excellent. For the SINE associated work, the main results of the team are: a) that SINE transcripts are capable of modulating biogenesis of endogenous miRNAs by engaging the miRNA processing machinery; b) that SINE transcripts can also affect stress responses in Arabidopsis by modulation the eIF2 kinase GCN2; and c) that the loss of the possible SINE RNA effectors DRB2 and DRB4 affects accumulation of p4-siRNAs but not SINE RNAs. For the LARP associated work, the major results of the group are a) the compilation and classification of the various LARPs found throughout eukaryotes into five distinct families; b) the discovery that the LARP4 and LARP6 families have undergone a neofunctionalization process, conserved through evolution, by which members of these families do or do not engage the mRNA associated factor PABP; and c) the description of a massive, LARP1 associated mRNA decay process during heat stress.

Given the journals in which these manuscripts have been published, the contributions of this group as collaborating authors on other manuscripts in high ranking journals (i.e. Science, PLoS Genetics), and the impact these manuscripts have had in the field of RNA biology (see below), the scientific quality and output of this team must be viewed as excellent. The team has also contributed two book chapters and a congress report.

Assessment of the team's academic reputation and appeal

The team's published work has been received very favourably; manuscripts devoted both to the SINE and LARP research have been cited extensively despite their relatively recent publication (three manuscripts already cited >20 times). The team has been active in acquiring funding (two major ANR BLANC grants as well as other smaller competitive awards) and have assembled an impressive list of international collaborators. A note must be made with respect to their special contribution to the field of LARP research; at least two of their manuscripts (Bousquet-Antonelli andDeragon, 2009 andMerret et al., 2013) investigating the evolutionary conservation of this superfamily now form the lens through which the rest of the international LARP research community focuses their analyses. The group has presented extensively at international conferences, has hosted three international conferences in the past five years and has been a major player in the founding the international LARP society. The team's senior members hold academic leadership positions (President of the National Committee for Research Plant Science; Member of AERES evaluation team; Secretary to the LARP Society) and serve on an editorial board of an internationally recognized research publication (Gene). The PI (often) and the CR1 (more recently) participate in thesis committees, juries and HDR examinations. Hence the team's academic reputation and appeal can be considered as outstanding.

Assessment of the team's interaction with the social, economic and cultural environment

For this criterion the team's activities can be considered as good, but with the following comments: The group participated in an open letter debating the social merits of genetically modified foods and was a regular contributor toward the internship of elementary and high school students (four intern students in the past four years). They also participated every year in the University organized "Fête de la Science". The current team leader serves as the Permanent Policy Officer for the Université de Perpignan affected to Agropolis International and is a member of their board of directors. Concrete progress in the development of economically viable and/or industry partnered research directions were however not reported.

Assessment of the team's organisation and life

The team is currently composed of 5 permanent staff: One PRCE, one CR1, one MCF, one AI and one TC. The team also mentored/is mentoring three Ph.D. students and five M.Sc. students, as well as two post-doctoral fellows. The team has overcome the departure of one CR1 through mobility, and the directorship of the group will change in 2015. For its size, the group is quite productive and so it is to be considered that the organization of the group works well.

Assessment of the team's involvement in training through research

The team graduated two Ph.D. students between 2008-2013, and another Ph.D. is continuing in the group. This is a good level of training for a team with one HDR and one recently obtained HDR. The team has also trained five M.Sc. students and four elementary/high school students. All the Ph.D. and post-doctoral trainees (including the ones still in the group) have peer-reviewed publications (usually multiple) and so the record of training must be considered as very good.

Assessment of the strategy and the five-year plan

While the previous period featured research on both SINE and LARP biology, the future plan has dropped work on SINE biology and focuses exclusively on the LARPs. This thematic change is described in the research plan as being partly due to the departure of the CR1 in the previous period, and may also have to do with the transition of the directorship of the group due in 2015. The thematic change toward LARP1 mediated and heat-stress associated changes in plant gene regulation is also rooted in the group's forthcoming attempts to revitalize the urgency and relevance of their research program vis a vis the effects of global warming on crop production. The future research directions [i) other stresses affecting mRNA degradation; ii) molecular mechanisms of stress mediated mRNA decay; iii) study of A. thaliana LARP6] are well reasoned, utilize international collaborators effectively and will likely produce significant results. Critically, the group has very recently demonstrated (Merret et al., 2013, now published in Cell Reports) that they have productively moved their LARP work from the realm of the largely computational into the wet lab, where most of their future research directions lie. As the number of research themes pursued by this group in the previous period will thus be diminished in the new period, maintaining the previous level of productivity may be challenging, at least initially. Promising preliminary data, as described in the report, suggest that the new research directions are on the right track. Hence, the research project can be considered as very good to excellent.

Conclusion

 Strengths and opportunities:

Strong previous productivity, strong record of funding and topical and engaging future research directions are good predictors for future success.

 Weaknesses and threats:

Changes to the theme and research directions pursued in the previous period may result in challenges in maintaining the previous level of productivity.

 Recommendations:

Collaborations already established (siRNA biogenesis; LARP structure; stress associated signalling) will assist in future research directions; with such a high investment for the future period in stress mediated decay, further collaborations with researchers with expertise in the fields of stress mediated decay, P-bodies and stress granules (still an emerging field) may enhance the likelihood of success. Ph.D. and postdoc training levels need to be maintained. The continued framing of these research directions in the context of topics with high relevance to society (i.e. global warming) should increase likelihood of support. The team may want to consider HDR certification for the MCF to ensure a steady continuity of future Ph.D. allocations. The team is encouraged to explore research directions conducive to alternative funding sources (industry/private sector). of them being first author on at least one high profile publication. Still unpublished is their recent work revealing that there is an alternative RdDM pathway that depends on the presence of AGO hooks in PolV for silencing of defined classes of transposable elements. Also unpublished is their work on the functional analysis of the de novo DNA methyltransferase DRM2. Both projects promise to lead to well-recognized publications. This short summary reveals that the team has an outstanding scientific output, reflected by a high number of high profile publications (in journals like PNAS, EMBO Reports and Molecular Cell) that concentrate on the question of RNA silencing mechanisms in plants.

Assessment of the team's academic reputation and appeal

The team is collaborating with many outstanding laboratories in the epigenetics field, thereby attesting an excellent academic reputation and appeal. This has been recognized by the experts appointed by the Region Languedoc Roussillon that delivered a grant to the team leader as a "chercheur d'avenir confirmé" in 2010. In addition, the team could secure three ANR grants (2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015) as well as a grant from the National Cancer Institute. The team leader was nominated as member of the CNRS evaluation board, as well as a member of the AERES evaluation committee for the IBP and GreD. He furthermore serves as reviewer for prominent journals in the field of epigenetics.

Assessment of the team's interaction with the social, economic and cultural environment

The team has participated in the "La Fête de la Science" from 2008 till 2011 and initiated several short projects for high school students to introduce them to modern plant research. The team furthermore contributed two articles to popularize plant research for the general public. The team leader is frequently participating in thesis committees. Concrete progress in the development of economically viable and/or industry partnered research directions are not reported. Hence the team's interaction with the social, economic and cultural environment can be considered as good.

Assessment of the team's organisation and life

The team is currently composed of 7 permanent people: 4 CNRS researchers (including PI), 2 CNRS AI and 1 PhD student. In addition there are 6 Master students. Each permanent researcher and PhD leads one project with the support of a technician/engineer or master student. Progress meetings are on a bi-weekly basis. Group members are also responsible for common platforms and stock managements.

Assessment of the team's involvement in training through research

The team had two PhD students between 2005 and 2013, a relatively low number in comparison to the other teams. In addition to that, the team currently has 6 master students. The team is furthermore organizing short research projects for high school students. Overall the involvement of the team in training can be considered very good.

Assessment of the strategy and the five-year plan

The team will focus in the next five years on three projects that are building on the results of ongoing research activities. In particular they will focus on the newly identified NERD silencing pathway and will, in collaboration with groups from the IBP (Institut de Biologie des Plantes) in Orsay, from the IJR (Institut Jean Roget) in Grenoble and from the Swiss Federal Institute of Technology in Zurich, dissect this pathway using genetics, molecular and biochemical tools. This project is supported by an ANR grant. A second focus will be on the characterization of the alternative RdDM pathway that depends on the presence of AGO (Argonaute) hooks in PolV. Also in this project (like in the first), the team plans forward genetic screening for mutants displaying altered silencing of a specific sensor. It is furthermore planned to continue the functional analysis of the de novo methyltransferase DRM2 and to characterize novel proteins containing an AGO hook domain. The experiments are logically designed and build on solid hypothesis and data. The team has established national and international collaborations with leading laboratories in the field (S. JACOBSSEN, USA; O. VOINNET, Switzerland; M.A. HAKIMI, France) who will support this research and by that increase the chance of success. Hence this research project can be considered outstanding.

Conclusion  Strengths and opportunities:

Strong team with high scientific productivity and quality. The team is well connected to the scientific community and focuses on well-defined questions. The team has been very successful to attract national grants.

 Weaknesses and threats:

No specific risk or threat at present that would specifically affect this team. However, the team has only a low number of PhD students and postdocs, which is surprising given its very high scientific productivity.

 Recommendations:

The recruitment of PhD students and postdocs should be enforced. Applications to alternative funding sources than ANR are encouraged (like EU funding). The team is co-directed by two experienced colleagues, one of them being close to retirement (2015): the future of the team will then rest on the shoulders of the most junior one. It is a small team consisting of 6 (soon 5) permanent staff members (1 DR, 1 PR, 2 MC, 2 lab IT -1 IE, 1 AI), all with a biology background, except for the IE who is a bioinformatician. For this 5 year period, 5 PhDs have been part of the team. There is a main take home message at the very beginning the team's report: the team has shifted his practice from mixed in silico+wet lab to bioinformatics. This is worth to be remembered and evaluated, as the current tendency is more on the opposite direction.

The theme of the team is plant genome analysis, with a historical special focus on Arabidopsis and rice. The emphasis is on genome structure with its two main driving forces: transposable elements & polyploidy. These two aspects reflect the interest of each co-director: TEs (Transposable Elements) for the junior PI, genome space for the more senior PI. As a result, this second aspect will be discontinued after his retirement in 2015. Seven main results are listed, the first four were under the junior PI leadership, the last three more related to the senior PI:

1. Impact of TEs on genome structure ; 2. Transpositional activity in the rice genome ; 3. Horizontal transfer of TEs ; 4. Annotation of TEs in genome projects ; 5. Impact of polyploidization on the evolution of gene space ; 6. Genome analysis of picoalgae and their viruses ; 7. Identification and characterization of AGO-hook proteins.

The work on the dynamic of TEs in Oryza is central in this activity with a novel and very interesting contribution on the detection of TE mobility and impact of TEs on genome size, all species included. It is indeed important to understand why some genomes are large and others not. Here we begin to have an answer on the timing of those events. What remains to be understood is what are the factors and mechanisms which allow or not TE invasion and maintenance which would control the species & strain variations in TE population. The horizontal transfer (HT) of TEs from one species to another one to escape death by species-specific silencing is a fruitful hypothesis and its testing is a promising aspect of the work of the team.

Due to its expertise on TEs, and the geographical proximity with Banyuls, team 3 has been involved in TE annotation in plants and green algae leading to 6 co-publications, the highest impact papers of the team and the whole lab. This part of the work resulted in a total of 17 publications and 5 reviews for these 5 years. Out of these 17 there are 6 papers in major journals (3 Plant J., 2 GBE, 1 BMC EvolBiol) in which the junior PI is the lead author and which therefore represent his own main scientific interests. The senior PI has played an important role in analyses on genome structure and polyploidization through the years and is still an important partner in collaborative projects on this topic with an obvious critical contribution today. It is also interesting to note that he is a co-author in many of the papers written in collaboration between different teams of the lab. We should not underestimate the importance of such colleagues which are often at the core of lab spirit and performance. It is thus hoped that his departure will be balanced by other people paying attention to the work of other teams, keeping lab spirit and cohesiveness. This part of the work ended up in 10 publications in which 3 as last author (1 MBE, 1 NAR, 1 BMC EvolBiol) and 2 reviews. As pointed out before, 6 out of these 10 publications are done in collaboration with other teams of the LGPDlab. This is altogether an excellent to outstanding record of publication. It is noteworthy that the papers are almost all from the PIs and PhDs, the two MCFs contributing to very few publications, including reviews, and only once as first or lead author. These MCFs may be overloaded by teaching activity; nevertheless it is for the team and for their own sake a bit problematic that they are not more involved and productive in research.

Assessment of the team's academic reputation and appeal

The junior PI has international recognition in the field of TEs, more specifically on retrotransposons and he is well integrated in the genomics network on monocots. Although the senior PI has maybe a bit less international recognition, it is remarkable that part of the initial work on genome duplication and polyploidization has emerged from his team, and that this interest has migrated to other places with a net benefit for research in France and worldwide. This reputation translates in the number of ANRs in which the team is involved, as well as the integration of the junior PI as partner in international plant genomic initiatives and as a member of the International Oryza network. The junior PIhas also given several oral presentations at different national and international symposia, meetings and workshops, several times as invited speaker as in the 9 th Int. Plant Mol. Biol. Congress in St Louis in 2009.

The junior PIhas also played an important role for UPVD, being Vice-President for research from 2008 to 2012 and being currently an elect member of its Scientific Council. He has been a member of two AERES French labs evaluation committees.

One may regret the lack of involvement of the team in any EU project, even as a simple participant. Also, it is to be noticed that no one in the team is member of the editorial board of a major scientific journal ("Rice" and "Frontiers in Plant Science" cannot be considered as major in this respect). In the same vein, the team PIs do not report either any involvement in committees evaluating international labs or projects, and not even in PhD thesis committees abroad. Altogether, this positions the team and its leaders among the excellent ones in term of reputation, but certainly not among the very best or exceptional.

Assessment of the team's interaction with the social, economic and cultural environment

The team's interaction with the social, economic and cultural environment can be considered as good but with the following comments:

The most important interactions of the group with the social and cultural environment was its participation to the scientific event "Fête de la Science".

There is a lack of interaction with any socio-economic partner, whatever the role in the economy or functioning of society (companies, institutions, public or private,...) which is by no way specific to this team but a general fact of for the whole LGDP lab. Many issues in the SWOT analysis have to be seen taking this "pure academic" behaviour into account.

Assessment of the team's organisation and life

This team is comparable in size with the other teams in the lab and is endowed with an adequate number of technical assistants. There is an efficient and nice working spirit in this team, as for the other teams in the unit. The two PIs supervized 5 PhD students, which is a pretty good number. Nevertheless, the MCFs are not mentioned in supervision and are involved in rather few publications.

Assessment of the team's involvement in training through research

Five PhD theses were defended in the last four years. The team shows also a good level of training at the Master degree. The team is involved in continuous education in bioinformatics for the whole unit. Hence this activity can be rated as very good.

Assessment of the strategy and the five-year plan

The perspectives of the team for the next five years are following two axis. First, investigating when transposition occurs in planta, during development and under external stimuli, namely stress. In terms of development, attention will be given to the germ line, to understand how genomic integrity will be kept, and on the existence of somatic diversity (TE load) as observed for humans. Response to stress will be investigated using natural populations, in a kind of evo-devo approach. Second, the investigation of HT of TEs will be continued, developing procedures to find it and searching it in wild plant populations. These proposals make sense given the background of the team and the current state of the art. They nevertheless involve experiments and sampling which remain costly (by their number) and labor-intensive: here the project is depending on good will of collaborators. As whole, the research project can be rated as very good to excellent.

Conclusion  Strengths and opportunities:

The team carries out basic research with a very good publication record. This was done through national and international collaborations as well as collaborations within the unit. Recognized expertise of the team leader in annotation of TEs allows co-publications in very high ranking journals. The proposed project builds on the expertise and knowledge of the group and offers new perspectives by looking into natural populations. It also fits with the will of the unit to focus on stresses. The team is well integrated into French and international networks which should allow maintaining and evening increase funding.

 Weaknesses and threats:

Weaknesses that could threaten this group include first the departure of one of the two who was playing an important stimulating and gluing role for the whole unit. A second concern is the too low involvement of the MCFs in the team, both in publications and in mentoring PhD students. A third and important concern is the lack of funding outside of French public agencies, including EU and contracts with the socio-economic sector, which concerns both financial resources and recruitment of post-docs.

 Recommendations:

The team is encouraged to maintain high level scientific research activities through its current expertise in TEs and extend this expertise keeping in mind the possibility to exploit findings in an ecological and/or socio-economical context. It should stimulate MDCs to defend a HDR in order to make the team more attractive towards students and better share the mentoring, publication writing and fund raising load. Last, the team as a whole could likely be more aggressive in searching for more diverse and international sources of funding. The team investigates the functions of thioredoxins and glutaredoxins in redox signalling, plant development and stress responses using reverse genetics approaches. The functions of distinct redoxins, located in either the nucleus, the cytosol or the organelles, have been studied within the group or in collaboration, showing their contribution to plant development, particularly in meristem development and hormone signalling. The characterization of mutants also demonstrated interplays between thioredoxin and glutaredoxin pathways.

In particular, during the past 5-year period, the team:

-showed the involvement of thiol reduction systems (TRX and glutathione) in meristematic activity and auxin signalling (Plant Cell 2010); -showed the formation of a Fe-S center in the GrxC1 glutaredoxin and its function in oxidative stress sensing (Plant Cell Environ. 2012); -contributed to the characterization of the backup function of the cytosolic TRX system in the reduction of gluthatione (PNAS 2009).

Overall, their results have been published in 12 research papers, 6 reviews (including an Annual Review of Genetics in 2009) and a book chapter. They have been communicated in 5 national or international conferences. These ouputs reflect a very good scientific quality of the team but with a relatively low number of publications. Nevertheless, as the other teams of the unit, the work is mainly published in journals of high rank, and benefited from fruitful collaborations.

Assessment of the team's academic reputation and appeal

The team has a large number (14) of French and foreign collaborators, attested by several collaborative papers during this time period. The team coordinated 1 ANR project (ANR Blanc Nucleoredox 2006-2010) and participated in 2 others. They also received fundings from the Agro Labex (2013-2014) and the PAI-ORCHID EGID program. The team's academic reputation as appeal on these grounds can be considered as very good.

The very good visibility of the team is also revealed by its involvement in the creation of the Thioredoxins and Glutaredoxins GDR2477 in 2002. Since then, they have been coordinating this GDR regrouping 14 French laboratories (including the organization of one GDR meeting/year). In this context the former PI and the current PI organized the "International Redoxin meeting" in Perpignan in 2009.

The group leader was co-editor of a Frontier in Plant Physiology topic (2013).

Assessment of the team's interaction with the social, economic and cultural environment The team's interactions with the economic and cultural environment can be considered as good but with the following comments:

The team regularly participated in "Fête de la Science" and one lecturer of the team was in charge of the "Science Village" of Perpignan University every year since 2007. During that period, many elementary or high school students were initiated to research through short stays in the team.

Concrete progress in the development of economically viable and/or industry partnered research directions are however not reported.

Assessment of the team's organisation and life

Weekly group meetings are organized where research projects are presented and discussed. One member of the group is in charge of the transgenesis technological platform of the unit.

Assessment of the team's involvement in training through research

During the reporting period, the group has trained 3 Master students, 4 PhDs. All four PhD students who defended their thesis during the reporting period have published.

The PI was member of 6 thesis committees, "rapporteur" of 7 thesis and "examinateur" of one.

Three members of the team are MCFs involved in teaching at the Perpignan University and one of them is coordinating a section of the Master 1 degree. This type of activity can be rated as very good.

Assessment of the strategy and the five-year plan

The proposed project is mostly in continuation with the work carried in the previous period. The group will aim at understanding how the cytosolic and nuclear thiol reduction systems modulate plant development in response to stresses. In particular, the team will study meristem activities and auxin signalling using the root as a model organ. Two main projects have been funded and will be performed during the next period: i) characterization of the crosstalk between thiol reduction systems and auxin pathways and its function in root development (funded by the Agropolis foundation), ii) characterization of the functions of redoxins in redox signalling (ANR Blanc "Cynthiol" coordinated by Graham Noctor). For the first project, forward and reverse genetics approaches together with real time redox status imaging techniques will be used. For the second project, reverse genetics will be coupled to omics (transcriptomics, proteomics, metabolomics) characterization of the mutants. The nucleoredoxin project is particularly original and they have little competition in this very interesting field.

The proposed strategy is coherent with previous approaches used by the group and can be rated as very good. The team is well integrated into French and international networks which should allow to maintain and even increase funding.

Conclusion

 Strengths and opportunities:

The team has a good record in the study of plant thioredoxins and glutaredoxins, using reverse genetics approaches. Taking into account that 3 members of the team have a rather heavy teaching load, the research is of very good level. The work plan for the next 5 years is feasible.

The research project linking redox signalling and development is original and in adequation with the expertise of the group and its collaborators.

 Weaknesses and threats:

The group is relatively small and includes 3 members with teaching duties. The numbers of PhD students and especially of post-docs are low.

Another possible threat would be the lack of success upon funding applications during the next contract. The remaining ANR project will end in 2016, the team has yet to secure additional funding.

Presently, the team's future relies on collaborative projects coordinated by other teams.

 Recommendations:

The team is encouraged to maintain high level scientific research activities, to lead fruitful collaborations and to maintain effort in grant applications to national and international programs.

 Detailed assessments

Assessment of scientific quality and outputs

The research of the team is concentrated on cellular and molecular mechanisms taking place in the nucleolus in Arabidopsis thaliana but will concern also crosstalk events between the nucleolus and the nucleoplasm. This team has experienced, at the beginning of the current term, the departure of the previous PI. He had strong visibility as a former director and for the work he developed on snoRNA (small nucleolar RNA) metabolism in plants. Hence, the work on nucleolar small RNAs has disappeared since the end of 2010 and led to only one publication (Plant Physiol) among the six publications of the team during the 2008-2013 term. This particular situation induced the team to reorganize its scientific project and focus on a more restricted study of the function of the nucleolus.

The scientific interest has been centred on nucleolar gene expression around two major themes: i) characterization of the machinery involved in pre-rRNA maturation and in control of rDNA transcription;

ii) organization and mechanisms for differential expression of rDNA genes.

Main results of the team include: i) Characterization of the protein composition of the U3 snoRNP, which is required for early co-transcriptional cleavages in the 5' ETS region of the 45S rRNA precursor. This work led to one publication in Plant Journal, but no functional study on the new identified components has been reported yet; ii) Identification of a protein (RTL2) belonging to the RNase III family of RNases and catalyzing the co-transcriptional cleavage at the 3'ETS of the precursor. This work was published in Nucleid Acids Research, and was continued in collaboration with two laboratories by studying members of this RTL family. One publication on this subject has been submitted; iii) Identification of polymorphisms within the multicopy 45S rRNA encoding genes and their classification in four variant groups. Implication of nucleolin for the differential expression of the rDNA genes was studied, leading to two publications (PloS Genetics, Nucleus), and one is in preparation. In addition, the leader participated to the writing of one chapter in a scientific book and two review articles.

The overall scientific quality and competence of the team is good but with a relatively low number of publications. Nevertheless, as for the other teams of the unit, the work is mainly published in journals of high rank, and benefited from fruitful collaborations.

Assessment of the team's academic reputation and appeal

The team's academic reputation and appeal has been assessed as very good to excellent. The team has indeed a very good visibility for its competence on the nucleolus in plant. This allowed its participation in two ANR projects as partner and allowed development of national collaborations. The PI of the team has maintained a productive and longstanding international collaboration on rDNA expression in A. thaliana with a strong team based in the US focusing on epigenetic phenomena, in particular nucleolar dominance. After obtaining his PhD in LGDP, the recently recruited CR2 was trained in this collaborating lab. Importantly, the team has enlarged its international and national collaborations towards laboratories working on nucleolar proteins in mammals.

The very good visibility is also revealed by several oral and poster presentations performed during international meetings and by the regular participation to thesis committees and juries. Nevertheless, the PI has had only one invitation for an international conference.

Assessment of the team's interaction with the social, economic and cultural environment One of the most important interactions of the group with the social and cultural environment was their steady involvement for short internships of Elementary and High School students, and their participation to the scientific event "Fête de la Science".

The MCF of the group has a major involvement in the life of the university as a deputy-director of the UFR Sciences and the Biology Department.

Concrete progress in the development of economically viable and/or industry partnered research directions are however not reported and therefore the team's interaction with the social, economic and cultural environment can be rated as good.

Assessment of the team's organisation and life

The posted size of the team is equivalent to the other teams of the unit, but some staff appears not to be fully engaged in scientific production. The PhD students are only supervised by the PI. The MCF has not been involved as co-supervisor.

The team has overcome the departure of one of the two initial PIs. Recruitment of the CNRS CR2 has helped to consolidate the team and forced to focus the scientific orientation on topics where the team excels. This reveals a good sense for scientific strategy and insures good bases for the scientific development of the team.

Assessment of the team's involvement in training through research One PhD thesis was defended in the last four years and one is on going, each with a good publication record. The team shows also a good level of training at the Master level. This indicates a very good activity in this respect.

Assessment of the strategy and the five-year plan

The objectives of the team are clear and well defined. The proposed project includes a logical follow up of the previous research in the field of stress sensing by the nucleolus and regulation of gene expression. Dynamic of rDNA chromatin structure under various conditions will represent one of the major themes. It will continue to benefit from past and recently established collaborations. The project includes exploration of an interesting new area of gene regulation. In particular, the team will investigate the potential role of the nucleolus to influence nuclear chromatin organization. Given the expertise of the CR2 in the approaches of fluorescence-activated sorting of nuclei and nucleoli, these innovative studies should provide interesting information. The conditions are favourable for the team to maintain and probably improve international competitiveness and scientific production. This will also contribute to maintain its attractiveness for PhD but also post-doc to carry out this very good to excellent research project.

Conclusion

 Strengths and opportunities:

The team carries out basic research with an average to good publication record. It was able to implement relevant collaborations outside the unit that helped publish their data in good to high-ranking journals. The proposed project builds on the technical expertise and knowledge of the group including a part of risk with the exploration of an interesting new hypothesis on gene regulation. Altogether, the project fits perfectly with the interests of the unit.

The CR2 researcher appears to be quite visible on the international scene and published articles in high ranking journals during his post-doctoral training. It represents a reinforcement of choice for the team.

The team obtained a significant level of financial support via national granting agencies. The leader has secured money for three years.

Hence the team has the potential to develop very strong and innovative science.

 Weaknesses and threats:

Weakness that could threaten this group include internal organization leading to a low record of scientific production. Willingness to publishing journal so high level is of course encouraged. But, the rate of publication over the five past years was quite low for some researchers of the team.

Another possible threat would be the lack of success in funding applications during the next contract. This would be a problem as the team has not yet developed relevant collaborations with other teams within the LGDP unit.

 Recommendations:

The team is encouraged to maintain high level scientific research activities, to support the young CR in the perspective to take Research Supervisor Qualification (HDR), to maintain effort in grant applications to national and international programs. The team is encouraged to explore research directions conducive to alternative funding sources (industry/private sector). No problem for this evaluation, everything went very smoothly, the committee thanks LGDP for the excellent organization of the meeting and especially the technical staff and administrative staff who have facilitated our connections to hotel and transport facilities.

  spent at least 12 months in the unit Number of Research Supervisor Qualifications (HDR) taken 2 Qualified research supervisors (with an HDR) or similar positions 8 7

  Transcriptional Gene Silencing and RNA silencing in plants Name of team leader: Mr Thierry LAGRANGE Workforce Permanent EPST or EPIC researchers and similar positions 4 4 N3: Other permanent staff (without research duties) 2 2 N4: Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors, etc.) N6: Other contractual staff (without research duties) spent at least 12 months in the team Number of Research Supervisor Qualifications (HDR) taken Qualified research supervisors (with an HDR) or similar positions 1 1  Detailed assessments Assessment of scientific quality and outputs The team has made major contributions to the RNA silencing field, starting with the identification of two plant-specific RNA Polymerases required for RNA dependent DNA methylation (RdDM, Genes and Dev. 2005). Since then, this team made several seminal contributions, with probably the most important one in the recent past being the identification of a novel DNA methylation pathway that has been proposed to target newly acquired and potentially active genomic regions. This work has been published twice in Molecular Cell (2012), with the team being the main contributor of one publication and collaborator of the other publication. Another outstanding contribution published in collaboration with the group of Mr Olivier VOINNET was to show that the human prion protein binds to argonaute and is involved in loading of the RISC complex (published in Nature Structural Biology, 2011). Also in collaboration with the VOINNET group they could show that viral suppressors bind to AGO1 and inhibit its function (Genes and Dev. 2010). They also made substantial contributions to identify new RNA silencing factors, published in Genes and Dev. 2007 and EMBO Rep. 2009, and characterized the mode of action of RNA PolV (RNA Polymerase V), published in PNAS 2009. The CR1 and CR2 researchers of the team are first or co-authors of the publications with all

N4:

  Permanent EPST or EPIC researchers and similar positions 1 N3: Other permanent staff (without research duties) 2 2 Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors

N3:N4:

  Functions of redoxins in plant development and stress responseName of team leader: Mr Jean-Philippe REICHHELD Workforce Permanent EPST or EPIC researchers and similar positions 1 1 Other permanent staff (without research duties) 2 1 Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors

Friday

Ms Cécile BOUSQUET-ANTONELLI Workforce Team workforce Number as at 30/06/2013 Number as at 01/01/2015 N1: Permanent professors

	and similar positions	2	2
	N2: Permanent EPST or EPIC researchers and similar positions	1	1
	N3: Other permanent staff (without research duties)	2	2
	N4: Other professors (PREM, ECC, etc.)
	N5: Other EPST or EPIC researchers (DREM, Postdoctoral students,
	visitors, etc.)
	N6: Other contractual staff (without research duties)	1

TOTAL N1 to N6 6 5 Team workforce Number as at 30/06/2013 Number as at 01/01/2015

	 Detailed assessments
	Assessment of scientific quality and outputs
	Doctoral students	2
	Theses defended	2
	Postdoctoral students having spent at least 12 months in the unit
	Number of Research Supervisor Qualifications (HDR) taken	1
	Qualified research supervisors (with an HDR) or similar positions	2	2
	

 Supervising bodies' general comments

1 ,  Mr.

End:

January 24, 2014, 14h

Visit site:

LGDP Université de Perpignan Institution:

Université de Perpignan Via Domitia, CNRS Address:

58 Avenue Paul Alduy, Perpignan

Specific premises visited

The members for the committee who stayed in the afternoon of Friday 25 th could visit the laboratories and platforms.

Conduct or programme of visit