Laurence Garczarek
email: laurence.garczarek@sb-roscoff.fr

Ulysse Guyet

Hugo Doré

Gregory K Farrant

Mark Hoebeke

Loraine Brillet-Guéguen

Antoine Bisch

Mathilde Ferrieux

Jukka Siltanen

Erwan Corre

Gildas Le Corguillé

Morgane Ratin

Frances D Pitt

Martin Ostrowski

Maël Conan

Anne Siegel

Karine Labadie

Jean-Marc Aury

Patrick Wincker

David J Scanlan

Frédéric Partensky

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motifs. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a Jbrowse viewer to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

INTRODUCTION

The regular decrease in sequencing costs associated with the rapid development of Next Genome Sequencing (NGS) technologies has led to the multiplication of microbial genomes (1, 2), making possible extensive comparative genomics studies. Genomes are generally annotated using gene calling programs, such as e.g. RAST [START_REF] Aziz | The RAST Server: Rapid annotations using subsystems technology[END_REF] or Prokka [START_REF] Seemann | Prokka: Rapid prokaryotic genome annotation[END_REF], which can provide fairly reliable annotations for the most conserved core genes involved in general metabolism (e.g., ribosomal proteins, Krebs or Calvin cycle enzymes, DNA replication, tRNA, etc.) or more specific but well characterized functions shared by many sequenced organisms (chlorophyll biosynthesis, nitrogen fixation, etc.). However, these automatic annotations are much less reliable for the least conserved accessory genes, such as those encoding enzymes responsible for cell wall biosynthesis that are often multi-domain, with highly variable domain composition, or those coding for species-or even strain-specific functions (e.g. biosynthesis of secondary metabolites, carotenoids, etc.). Thus, even though an initial step of automatic annotation is mandatory, functional annotation of predicted coding sequences (CDS) still requires extensive expert human curation to be reliable, especially for non-model organisms. With the exponential increase of newly sequenced genomes, manually curating individual genomes is however a highly time-consuming and inefficient approach. A smart alternative is to curate several phylogenetically related genomes at a time, after gathering sequences into Clusters of Likely Orthologous Genes (CLOGs), i.e. genes that exhibit reciprocal best hits to one another and are hypothesized to have the same function in the different members of the dataset [START_REF] Galperin | Expanded microbial genome coverage and improved protein family annotation in the COG database[END_REF][START_REF] Huerta-Cepas | EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses[END_REF]. This strategy, notably used in the NCBI's 'prokaryotic genome annotation pipeline' [START_REF] Tatusova | NCBI prokaryotic genome annotation pipeline[END_REF] for annotating new genomes or re-annotating older genomes before inclusion in the RefSeq database, allows propagating rich, functional annotations made at CLOG level to all proteins composing the CLOG and makes it possible to unify and standardize these annotations across all sequenced strains.

Here we present Cyanorak v2.1, an information system based on CLOGs that is dedicated to the annotation, comparison and visualization of picocyanobacterial genomes.

Initially created in the mid 2000's by A. Dufresne and co-authors to compare the first 14 genomes of marine and brackish picocyanobacteria [START_REF] Dufresne | Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria[END_REF], the Cyanorak database has significantly increased since then and relies on a completely redesigned and tremendously enriched information system (v2.1) which, contrary to Cyanorak v1, is scalable, i.e. conceived to allow addition of more genomes. The current database encompasses 95 genomes and two metagenome-assembled genomes (MAGs), including 31 newly released Synechococcus and Cyanobium genomes [START_REF] Doré | Evolutionary mechanisms of genome diversification in marine picocyanobacteria[END_REF], which have been closed using a customdesigned assembly and scaffolding pipeline [START_REF] Farrant | WiseScaffolder: An algorithm for the semi-automatic scaffolding of Next Generation Sequencing data[END_REF]. All strains whose genomes have been included in the Cyanorak v2.1 database belong to Cyanobacteria Subsection I, Cluster 5 sensu Herdman [START_REF] Herdman | Form-genus XIII. Synechococcus[END_REF], a short-rod shaped group that forms a deep monophyletic branch within this ancient phylum [START_REF] Shih | Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing[END_REF]. The common ancestor of all Cluster 5 members is thought to have diverged from other cyanobacteria about 1 Gy ago, during the Mesoproterozoic period [START_REF] Sánchez-Baracaldo | Origin of marine planktonic cyanobacteria[END_REF]. Members of Cluster 5 are also called 'α-cyanobacteria', based on the occurrence in their cytoplasm of specific α-type carboxysomes, phylogenetically and structurally closer to that of thiobacilles than to the β-type carboxysomes found in all other cyanobacteria, so-called 'β-cyanobacteria' [START_REF] Badger | CO2 concentrating mechanisms in cyanobacteria: Molecular components, their diversity and evolution[END_REF]. Cluster 5 itself is split into four major groups, including the monophyletic, strictly marine Prochlorococcus lineage and three deeply branching groups, called sub-clusters (SC) 5.1 through 5.3 [START_REF] Dufresne | Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria[END_REF][START_REF] Huang | Novel lineages of Prochlorococcus and Synechococcus in the global oceans[END_REF][START_REF] Scanlan | Ecological genomics of marine picocyanobacteria[END_REF]. Based on the comparison of 81 non-redundant genomes, Doré and coworkers recently suggested to rename them Ca. Marinosynechococcus (SC 5.1), Cyanobium (SC 5.2) and Ca.

Juxtasynechococcus (SC 5.3) (9). SC 5.1 is the most diversified of all these lineages, with about 10 phylogenetically distinct clades based on 16S rDNA phylogeny ( 16) and 11 to 16 using higher resolution markers [START_REF] Ahlgren | Diversity and distribution of marine Synechococcus: Multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean[END_REF][START_REF] Mazard | Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus[END_REF]. Members of these clades are all strictly marine except clade VIII that specifically gathers halotolerant strains. SC 5.2 also mostly encompasses halotolerant strains as well as one freshwater representative (Cyanobium gracile PCC 6307). While members of SC 5.3 were initially thought to be strictly marine [START_REF] Dufresne | Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria[END_REF][START_REF] Scanlan | Ecological genomics of marine picocyanobacteria[END_REF], freshwater members of this group were recently discovered in various lakes (19,[START_REF] Cabello-Yeves | Ecological and genomic features of two widespread freshwater picocyanobacteria[END_REF].

The current version of Cyanorak v2.1 encompasses representatives of most of the lineages (SC and clades) known to date in Cluster 5, with the exception of the newly described freshwater members of SC 5.3 as well as members of the yet-uncultured SC 5.1 clades EnvA and EnvB [START_REF] Mazard | Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus[END_REF][START_REF] Farrant | Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria[END_REF]. Since all Cluster 5 members possess a similar morphology (spherical to rod shaped) and lifestyle (aquatic, non-diazotrophic oxyphototrophs; [START_REF] Herdman | Form-genus XIII. Synechococcus[END_REF]) and form a monophyletic branch within the Cyanobacteria phylum, we assume that members of most CLOGs defined within this genetically homogeneous group exhibit the same function, though this may not be true when considering more distant organisms, notably cyanobacteria exhibiting different lifestyles. Here, we describe the construction of the Cyanorak v2.1 database, the rich functional annotation available for each CLOG and the tools and plugins that were developed to explore the genomic diversity of this ecologically relevant group of organisms, which has recently become one of the main microbial models in marine ecology.

MATERIALS AND METHODS

Clustering of likely orthologous sequences and CLOG curation

Following the construction of a first series of CLOGs based on the 14 first sequenced picocyanobacterial genomes [START_REF] Dufresne | Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria[END_REF], Cyanorak v1 CLOG numbers have been cited in a number of publications from our group (see e.g., [START_REF] Partensky | Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex[END_REF][START_REF] Partensky | Prochlorococcus: Advantages and limits of minimalism[END_REF][START_REF] Mella-Flores | Prochlorococcus and Synechococcus have evolved different adaptive mechanisms to cope with light and UV stress[END_REF][START_REF] Kolowrat | Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511[END_REF][START_REF] Humily | A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus[END_REF][START_REF] Garczarek | Function and evolution of the psbA gene family in marine Synechococcus: Synechococcus sp. WH7803 as a case study[END_REF][START_REF] Breton | Unveiling membrane thermoregulation strategies in marine picocyanobacteria[END_REF][START_REF] Blot | Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress[END_REF][START_REF] Pittera | Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus[END_REF]). In order to preserve at best these preexisting CLOG numbers after the addition of 83 new genomes either retrieved from Genbank or newly sequenced at our initiative (Fig. 1; (9)), all genes from the 97 genomes were first clustered using all-against-all BLASTP+ comparison [START_REF] Altschul | Basic Local Alignment Search Tool[END_REF] and the OrthoMCL clustering algorithm [START_REF] Li | OrthoMCL: Identification of ortholog groups for eukaryotic genomes[END_REF] with an e-value threshold of 10 -5 and new CLOGs were then mapped to previously defined Cyanorak v1 CLOGs. New CLOGs containing all sequences from a v1 CLOG plus additional sequences from new genomes as well as manually curated CLOGs were assigned the previous v1 CLOG numbers. All other sequences were then tentatively assigned to preexisting CLOGs using HMMER [START_REF] Finn | HMMER web server: Interactive sequence similarity searching[END_REF] with an e-value threshold of 10 -20 and remaining sequences were finally clustered using OrthoMCL to define new CLOGs or left as singletons in individual CLOGs if not clustered.

Since Cyanorak v1 contained only CDS, these steps also allowed us to generate CLOGs for rRNAs, tRNAs, tmRNAs using all-against-all BLASTN+ and the OrthoMCL algorithm using the same threshold as for CDS [START_REF] Li | OrthoMCL: Identification of ortholog groups for eukaryotic genomes[END_REF]. After this semi-automatic clustering step, a large number of CLOGs (about 4,300, i.e. 17 % of all CLOGs; Fig. S1) were further manually curated in order to i) check and complement the functional description of CLOGs and ii) verify that members of a given CLOG were truly orthologs, based on their phyletic pattern, alignments and phylogenetic trees. Paralogs were moved into different CLOGs when they grouped together into different branches as the bona fide orthologs. In order to refine assessment of the core genome [START_REF] Doré | Evolutionary mechanisms of genome diversification in marine picocyanobacteria[END_REF], more than 1,750 genes missed by gene prediction software tools, either because they were too short (e.g. petM, psbM) or partially overlapping with other genes notably in the case of long 3'-3' overlaps (e.g. for pyrB-ndbA or panB-hemN), were also manually added to different genomes. Furthermore, many overpredictions of ORFs (e.g., short CDS of unknown function totally overlapping long annotated CDS) were eliminated, and this even from genomes retrieved from Genbank. Finally, many start positions were corrected from sequences obviously too short or too long, based on an alignment of all CLOG members and/or 5'-end extensions using TBLASTN searches.

Implementation of the Cyanorak v2.1 information system

The development of Cyanorak v2.1 was done in two steps. The first version (v2.0) of this information system included a history feature to keep track of every change and allowing to readily revert any change at a very granular level as well as enabling curators to check the journal of changes undergone by every gene or CLOG. This private version of the information system is still currently used for the manual curation of the database. However, in order to give the general public access to the curated data with the best possible response times, especially now that the number of genomes and MAG's in the database has risen to 97, a completely new version of the Cyanorak information system, devoid of the history feature (v2.1), was recently developed and proved to be two to three times faster than v2.0.

Two instances of the Cyanorak information system therefore co-exist on our server: i) the restricted access, editable Cyanorak v2.0 version allowing expert curators to edit most fields of the 'CLOG' and 'gene' pages, and ii) the publicly accessible, non-editable Cyanorak v2.1 version, the latter corresponding to the state of the Cyanorak database at the time of publication of a comparative genomics study of the 81 non-redundant, high quality genomes of the database (9) and of an extensive transcriptomic analysis of the response of the Synechococcus sp. WH7803 strain to various environmental stresses [START_REF] Guyet | Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803[END_REF]. This public version will be regularly updated in the future, with concomitant changes in version number, when new whole genome sequences (WGS), single amplified-and metagenome assembled-genomes (SAGs, MAGs) and/or transcriptomes either retrieved from public databases (e.g. Genbank) or generated by our group will be added to the Cyanorak database and described in the frame of forthcoming publications. A restricted access, editable instance based on the v2.1 implementation is currently being developed and should replace the current v2.0 instance in the near future for expert curation purposes.

On a technical level, the bulk of the Cyanorak v2.1 has been implemented using the Java programming language, with an extensive use of the Spring framework. The data itself is stored in a relational database (PostgreSQL), and the link between the application and the database is done through an object relational mapper (Hibernate). A small set of Python auxiliary tools has also been developed, mostly to prepare the data for import, to postprocess exported data or to perform specific batch updates.

RESULTS

General characteristics of the database

Built from 97 picocyanobacterial genomes, including 43 Prochlorococcus and 54 Synechococcus/Cyanobium, which are representative of the wide genetic and pigment diversity existing within these genera (Fig. 1), Cyanorak v2.1 encompasses 252,176 genes that were split into 25,834 CLOGs. A plot of the distribution of the number of sequences per CLOG expectedly shows that the most frequent categories are CLOGs with one sequence, i.e. unique genes (15,283 CLOGs), and CLOGs with few (2 to 5) members (Fig. S1).

Although most of these CLOGs (e.g. 91% of unique genes) are annotated as "hypothetical" or "conserved hypothetical" proteins, a number of them display a more precise functional annotation, since they share some similarities to genes or domains of known function, with among the most abundant: glycosyltransferases, restriction-modification system proteins, integrases, transposases, methyltransferases, NAD-dependent epimerases/dehydratases and tetratricopeptide repeat (TPR) family proteins. The next most abundant CLOG category (611 CLOGs) is the one containing 97 sequences, which corresponds to the picocyanobacterial core genome sensu stricto. As expected, this number is significantly lower than the picocyanobacterial strict core gene set (911 genes) estimated by Doré et al. [START_REF] Doré | Evolutionary mechanisms of genome diversification in marine picocyanobacteria[END_REF] using the 81 non-redundant, high-quality genomes of the Cyanorak database. Yet, given that some of the 97 genomes or MAG's, especially those not included in this 81-genome set, are incomplete and/or contain frameshifted genes (in this case, the two or more gene fragments resulting from a frameshift have been put into the same CLOG), many CLOGs contain a number of genes that is close but not exactly equal to 97. So, the picocyanobacterial core genome sensu lato is likely much larger than 611 genes, and we estimated it using a relaxed definition of core genes (CLOG is considered as core of a taxonomic group if it is present in ≥ 90% of the strains within this group) to be 1271 genes.

A small number of CLOGs contain a large number of sequences, i.e. between 105 and 337 sequences. These CLOGs most often contain paralogous sequences that cannot be split into different CLOGs based on phylogenetic analyses. These notably include the identical multi-copy genes coding for the photosystem II core proteins D1.2 and D2, porins, AbrB-like transcriptional regulators and the high-affinity phosphate-binding protein PstS.

Cyanorak web interface and tools

The homepage of the Cyanorak v2.1 information system shortly describes the origin of the genomes used to build the CLOGs database, the history of its construction and the main references that used it. The top banner available from all pages encompasses several clickable menus, including the 'organisms page' that lists the different genomes of the database and their characteristics, a 'search page' with different options to access the CLOG or gene pages of interest, a 'BLAST scroll down menu', a JBrowse menu giving access to direct links to the viewer of each genome, as well as several other menus providing useful information about the database (Previous Versions, References, Links, About us).

Organisms page

The 'organisms page' consists of two tables, the first one listing Prochlorococcus genomes and the other one Synechococcus and Cyanobium genomes. They provide taxonomy, pigment type, sequencing center as well as various genomic characteristics (size, GC%, status, accession numbers, number of CDS, etc.) for each genome included in the database.

Next to each strain name is a clickable 'J' logo that gives access to the JBrowse page of the corresponding genome (see below). A distribution map of all of the strains drawn with OpenStreetMap® (https://www.openstreetmap.org/) is also available in this section (Fig. 2), offering a flexible set of options to focus on individual strains or to select all or a subset of Prochlorococcus and Synechococcus/Cyanobium strains. Strains collected in nearby locations can also be shown with a single marker to enhance readability. In this section, each strain name in the Table can be clicked to get more detailed information (e.g., isolation site, isolator, environment ontology (ENVO) code, etc.) and also allows the user to export gene and protein sequences in FASTA format as well as whole genomes in Genbank format.

In each of these files, the annotation of every gene corresponds to that found on CLOG pages (see below), which was given priority over the initial gene annotation, even if the genome was retrieved from Genbank.

Genomic Search tools

The main entry to the Cyanorak v.2.1 database content is through the 'genomic search' menu, with three possible options. The first one is a 'quick search' of any term mainly through 'cluster number', 'gene names' and 'product descriptions' fields, a term that can be searched either as an exact match or as a pattern in a more complex sentence. For instance, a search for 'dna' in 'pattern' configuration will provide a list of CDS clusters whose gene name annotation includes 'dna' (e.g. dnaA, dnaB, etc.) as well as a list of products whose description includes DNA (e.g. DNA gyrase, formamidopyrimidine-DNA glycolase, etc.).

Search results are organized in three distinct tabs. The first one lists the matching clusters, the second one lists the matching CDS and the third one lists the matching RNA entries.

Each list gives the essential information about every match and provides links to access detailed descriptions of these entries. The 'advanced search' option allows the user to look into any field documented in the CLOG, CDS or RNA pages, including functional categories (e.g., EC or K number, InterPro entries, GO terms, etc.) and to select one, all or a specific set of strains. Finally, the 'phyletic pattern search' option is used to search for CLOGs, CDS and RNA that are shared by a selection of genomes and that can be either present or absent in other strains depending on the selected option. This search option is for instance most useful to identify genes specific to a particular strain combination such as all Prochlorococcus, a given clade or a given pigment type.

CLOG page

By clicking on a Cyanorak CLOG number (format: CK_XXXXXXXX) in the result list of any search (see above), the user is sent to a cluster page providing a full description of the function and phyletic pattern of the corresponding CLOG. An indication in the upper right corner of the CLOG page specifies whether the CLOG has been manually annotated, i.e.

whether an expert has edited and validated its sequence content and functional annotation.

The cluster page contains several fields, including from top to bottom: i) the corresponding gene identifier in the Cyanorak v1 database (if any), generally corresponding to the last digits of the Cyanorak v2.1 CLOG number, ii) a gene name and its synonyms (if any) as well as the product description, iii) functional categories including COG [START_REF] Galperin | Expanded microbial genome coverage and improved protein family annotation in the COG database[END_REF] and EggNOG [START_REF] Huerta-Cepas | EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses[END_REF] identifiers and their description, CyOG number (as reported in (35)), Enzyme Commission (EC) and K numbers referring to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (www.kegg.jp), 'TIGR Roles' and custom-designed 'Cyanorak Roles', the latter being largely derived from 'TIGR Roles' but providing more details on photosynthetic and other key cyanobacterial processes, as well as gene ontology (GO) terms and their description; iv) results of protein domain and motif searches, including TIGRFAMs, PFAMs, ProSite patterns and profiles, as well as InterPro entries, v) numbers of related CLOGs, i.e. possible paralogs, and vi) a phyletic pattern providing the distribution of the genes in the different genomes, classified by taxonomy (genus, clade and, for Synechococcus SC 5.1 strains only, subclades, according to ( 18)), and indicating the pigment type of the corresponding strain (Fig. S2, [START_REF] Humily | A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus[END_REF][START_REF] Grébert | Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria[END_REF][START_REF] Moore | Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates[END_REF]). The bottom of the page lists ORF_IDs of the different members of the CLOG, with their initial annotation, a useful piece of information when the annotation was made either automatically or by other research groups.

On the top left of the 'cluster page' is a link to the 'genomic context', which displays the four genes upstream and downstream of the selected gene in all members of the CLOG.

Two possible representations of the context are accessible through a toggle button: genes are shown either all at the same size or in relative size (Fig. 3A-B). To ease comparisons, the central gene is always represented in forward direction whatever its original direction in the genome and the context is arranged accordingly. Each CLOG has a given (random) color and background (plain or stripped) and genome context can be regenerated around any gene of the current context by clicking on the ORF_ID of the corresponding gene, while clicking on a CLOG number opens the corresponding CLOG page.

Links at the bottom of the cluster page allow the user to export all sequences of the CLOG at once as an amino acid or nucleotide FASTA file. The descriptor of each sequence in the export is standardized and provides the genus abbreviated to the three first letters (Cya|Syn|Pro); strain name; SC, clade or subclade depending on the finest taxonomic level available for the strain as in [START_REF] Farrant | Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria[END_REF]; pigment type as in [START_REF] Grébert | Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria[END_REF]; Cyanorak ORF_ID; gene positions and strand in the genome; Cyanorak CLOG number and gene name if any (e.g. >Syn_A15-24_IIIa_3c|CK_Syn_A15-24_02629:2153016-2154431:1|CK_00000125|dnaB).

Gene page

By clicking on any gene in the cluster page or the relevant search result tab, the user accesses the 'gene page', which includes most fields previously described for the CLOG page. Specificities compared to the latter include i) the source and location of the gene, namely the strain name, contig and gene location (position and strand) on the contig, generally consisting of the whole chromosome, ii) a series of identifiers in Cyanorak and, if relevant, in other databases (Genbank, RefSeq, etc.) and iii) the gene sequence in nucleotides and (for CDS) in amino acids. It must be stressed that this page contains the initial annotation of the gene (e.g. if the genome was retrieved from Genbank), and the latter often differs from the CLOG annotation which is typically much more extensive, especially if the cluster was manually curated. All genes included in Cyanorak (even when retrieved from public databases) were given, in addition to their initial ORF_ID, a unique Cyanorak ORF_ID with the standardized format CK_Genus_Strain_XXXXX (e.g. CK_Syn_PROS-U-1_00601) in order to normalize gene names and ease the identification of the genome source. Also noteworthy is that the genomes included in Cyanorak, even those that have been sequenced by other groups, have all been manually curated to some extent, including predictions of missing genes or removal of wrong predictions, and thus differ from their counterparts in other public databases (Genbank, RefSeq, etc.) not only regarding their annotation (made at CLOG level) but also their gene content.

BLAST

An indispensable complement to the Cyanorak database is the possibility for users to search any sequence in all genomes or proteomes of the database using two BLAST options available from a BLAST scroll down menu. This includes an implementation of the BLAST algorithm using the SequenceServer graphical interface [START_REF] Priyam | Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases[END_REF] allowing to blast one or several nucleotide or protein sequence(s) against a selection of up to 97 genomes ('Blast a selection') or all genomes ('Blast all'). Results of a Blast search returns the Cyanorak ORF_ID, the strain taxonomy (at the SC, clades and/or subclade level) and pigment type, the CLOG number as well as the CLOG gene name and product (e.g. CK_Syn_A15-24_00652_III_IIIa_3c CK_00001060!rpoC1!DNA-directed RNA polymerase complex, gamma subunit).

JBrowse page

Clicking on the 'J' logo next to each strain name in the JBrowse page (or 'Organisms' page) gives access to a JBrowse viewer [START_REF] Buels | JBrowse: A dynamic web platform for genome visualization and analysis[END_REF] allowing the user to visualize the whole annotated genome and to zoom in to see the local context and detailed annotation of any gene, as derived from the 'CLOG page' (see above). Right clicking on a gene gives access to the detailed functional annotation of the corresponding gene, as derived from the cluster page in Cyanorak, with hyperlinks to Cyanorak and external functional databases. The genes can be searched by annotation or Cyanorak ORF_ID. A 'select tracks' menu gives access to additional data associated with each genome, when available. These include strict and large core and accessory genomes, gained genes as well as genomic islands, as determined in a recent comparative genomic study of 81 non-redundant picocyanobacteria genomes [START_REF] Doré | Evolutionary mechanisms of genome diversification in marine picocyanobacteria[END_REF]. Also available are operon predictions using ProOpDB [START_REF] Taboada | ProOpDB: Prokaryotic operon database[END_REF] and transcriptomic data. The latter can be visualized by experiment, acclimation conditions (e.g. low or high light) or stress conditions (e.g. exposure to low temperature or UV radiations). In the current version of Cyanorak, transcriptomic data are only available for Synechococcus sp. WH7803 [START_REF] Blot | Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress[END_REF][START_REF] Guyet | Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803[END_REF] and a number of other Prochlorococcus or Synechococcus strains studied by other groups, but in this case expression data are only displayed as log2(Fold Change).

Exports

Various exports are available from different pages of the Cyanorak v2.1 information system, including strain and genome characteristics from the organism page, annotated complete genomes from the individual strain pages, individual fasta protein and nucleotide sequences from gene pages and multifasta protein and nucleotide sequences from cluster pages.

DISCUSSION

As the most ancient photosynthetic organisms, cyanobacteria had a key role in the oxidation of the primitive Earth atmosphere [START_REF] Lyons | The rise of oxygen in Earth's early ocean and atmosphere[END_REF] but also in the primary endosymbiosis, an event that led to the advent of green and red algae and ultimately to all eukaryotic oxygenic phototrophs [START_REF] Archibald | The evolution of algae by secondary and tertiary endosymbiosis[END_REF]. Besides their relevance in evolutionary biology, cyanobacteria are also of great interest in ecology, given their ubiquity and abundance in many ecosystems, including oceans and deserts [START_REF] Garcia-Pichel | Estimates of cyanobacterial biomass and its distribution[END_REF] and the noxious impacts of their bloom-forming toxic representatives in freshwater environments [START_REF] Huisman | Cyanobacterial blooms[END_REF]. For all these reasons, but also thanks to their fairly small genomes sizes, ranging from 1.4 to 11.6 Mbp, these microorganisms have been the subject of many sequencing projects [START_REF] Dufresne | Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria[END_REF][START_REF] Shih | Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing[END_REF][START_REF] Kettler | Patterns and implications of gene gain and loss in the evolution of Prochlorococcus[END_REF], which in turn triggered the generation of a number of dedicated genome databases. The oldest of these databases is Cyanobase (http://genome.microbedb.jp/CyanoBase), initially created to provide access to the first sequenced cyanobacterial genome, the model freshwater strain Synechocystis sp. PCC6803 [START_REF] Nakamura | CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803[END_REF][START_REF] Fujisawa | CyanoBase: A largescale update on its 20th anniversary[END_REF]. This database has since then been extended to host many more recently sequenced freshwater and marine cyanobacterial genomes (376 entries, including 86 complete genomes in April 2019), but has been 'under maintenance' since summer 2019.

Although this database provides much useful genomic information, this is not a CLOG database and is therefore not designed to make extensive genomic comparisons. Also worth noting, CyanoClust (http://gclust.c.u-tokyo.ac.jp/CyanoClust/) is a database of homologous groups initially limited to cyanobacteria and plastids and which was more recently extended to a heterotrophic bacteria and Archaea [START_REF] Sasaki | CyanoClust: comparative genome resources of cyanobacteria and plastids[END_REF]. It provides lists of orthologs generated by the program Gclust, but functional annotation is limited to the original product description and fasta sequence of individual members of each CLOG. The database that was most similar to Cyanorak v2.1, was the 'Prochlorococcus portal' a.k.a. 'Proportal' [START_REF] Kelly | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage[END_REF]. It was also based on CLOGs computed from a number of Prochlorococcus and marine Synechococcus genomes, with a strong focus on the former genus. Since 2018, this database has however been merged to the Joint Genome Institute Integrated Microbial Genomes and Microbiomes (JGI-IMG) and renamed 'IMG-Proportal' (http://img.jgi.doe.gov/cgi-bin/proportal/main.cgi).

The latter site lists all publicly available genomic, transcriptomic, metagenomic and population data on Prochlorococcus, Synechococcus and their cyanophages, which can be analyzed using the IMG's data warehouse and comparative analysis tools [START_REF] Markowitz | IMG 4 version of the integrated microbial genomes comparative analysis system[END_REF], but the initial CLOG-centered organization of Proportal has been lost.

Compared to these databases, Cyanorak is more function-oriented and aims to provide rich and up-to-date functional annotations of CLOGs, with a preference for those derived from genes or proteins that were characterized in cyanobacteria. In contrast to most large CLOG databases currently available, such as COG [START_REF] Galperin | Expanded microbial genome coverage and improved protein family annotation in the COG database[END_REF] or EggNOG (6) that encompass very distantly related organisms, Cyanorak is focused on Prochlorococcus and marine Synechococcus/Cyanobium, i.e. a monophyletic and homogenous group of microorganisms sharing a similar morphology and lifestyle, making more reliable the assumption that reciprocal best hits in different genomes truly correspond to orthologs. Thanks to this CLOGbased approach, the continuous expert curation efforts employed since the mid-2000's have allowed us to improve the annotation of all genomes of the Cyanorak database, even those initially retrieved from Genbank. Furthermore, a number of genes that were missing in these often automatically annotated genomes have been added, while many over-predictions have been suppressed, so that both gene content and annotations differ between genomes in Cyanorak and their counterparts in large public databases.

Another important asset of Cyanorak is the variety of tools for exploring and exporting genomes from the database. For instance, one can search for CLOGs common or specific to a particular phylogenetic group of interest, an approach that can provide clues to identify genes coding for a specific function. For instance, searching Cyanorak for homologs of MpeZ, an enzyme involved in type IV chromatic acclimation (CA4), i.e. a reversible pigmentation change occurring in some Synechococcus strains when shifted from blue to green light [START_REF] Huisman | Cyanobacterial blooms[END_REF], allowed us to identify a second type of chromatic acclimation, so-called CA4-B, which possess MpeW, a MpeZ homolog. Both the mpeZ and mpeW genes are located in a specific genomic island, but gene content, organization and genomic context differ between the CA4-A and CA4-B islands [START_REF] Humily | A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus[END_REF]. Another interesting example concerns the chlorophyll (Chl) biosynthesis pathway. It is well known that Prochlorococcus lacks monovinyl-Chl a, which is replaced by divinyl-Chl a, even in reaction centers [START_REF] Goericke | The pigments of Prochlorococcus marinus : the presence of divinyl chlorophyll a and b in a marine prochlorophyte[END_REF]52).

Comparing the genomic context of the core malQ gene (encoding a glucanotransferase) between all genomes of the Cyanorak database shows that in marine Synechococcus this gene is always preceded by an enzyme that reduces divinyl-Chl a into mononyl-Chl a, but surprisingly there are two possible mutually exclusive reductase genes depending on strains, either dvr [START_REF] Nagata | Identification of a vinyl reductase gene for chlorophyll synthesis in Arabidopsis thaliana and implications for the evolution of Prochlorococcus species[END_REF] in strains from clades I-IV, VII, CRD1, WPC1 XX and UC-A or cvrA [START_REF] Islam | slr1923 of Synechocystis sp. PCC6803 is essential for conversion of 3,8divinyl(proto)chlorophyll(ide) to 3-monovinyl(proto)chlorophyll(ide)[END_REF] in all other Synechococcus/Cyanobium lineages (Fig. S3). Dvr and CvrA possess the same enzymatic function but share no sequence identity, and are thus analogs. In Prochlorococcus genomes, neither dvr nor cvrA are found upstream of malQ, and none of these genes is found elsewhere in the genome, explaining why these strains are all incapable of producing monovinyl-Chl a.

Cyanorak v2.1 is also a repository for a variety of transcriptomic data, the interpretation of which relies heavily on the quality of genome annotation. In Cyanorak, these data are connected to the genome database through a JBrowse interface, which also gives access to genomic features such as predicted operons, gained genes or the core or accessory nature of genes, which can be used to further refine the interpretation of gene expression data (see e.g. ( 34)).

FUTURE DEVELOPMENTS

The current version of the database includes rRNAs, tRNAs and tmRNAs, but still no small RNAs (sRNAs), so we plan to add such information in a forthcoming release, at least for the most conserved sRNAs. Another planned improvement of the database concerns the curation of gene starts. Although many gene starts have been corrected manually, amino acid alignments readily made from exports of CLOG pages show that a large number of those starts are still mis-predicted, leading to seemingly too short or too long sequences in a number of genomes. We will thus develop an application that allows to automatically correct likely wrong starts, at least when N-termini are not too variable. Finally, new fields will be added on the CLOG page, including for instance orthologs of each CLOG in relevant biological models, such as the freshwater cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7942, the heterotrophic bacteria Escherichia coli and Bacillus subtilis or the higher plant Arabidopsis thaliana.

Future versions of the Cyanorak database will include a number of transcriptomes for several Synechococcus strains recently generated by our team but that are still unpublished as well as genomes newly released from public databases. It must be stressed that the aim of Cyanorak is not to host all of the rapidly-growing number of incomplete SAGs and MAGs, apart from a few representative uncultivated lineages (e.g., Synechococcus EnvA/B, Prochlorococcus HLIII-VI). Thus, a pipeline is currently being developed to easily transfer the rich functional annotation of the Cyanorak genomes to these new partial genomic sequences and, more generally, to any picocyanobacterial environmental reads retrieved from metagenomes and metatranscriptomes. A few previous studies, where annotations made in Cyanorak were used to analyze omic data, have notably allowed us to i) compare the nitrogen assimilation capacities of Prochlorococcus populations from inside and outside the Agulhas rings in the South Atlantic Ocean (55), ii) highlight differences between Prochlorococcus and Synechococcus populations in their adaptation and acclimation responses to iron deficiency in the vicinity of the Marquesas island (56) and iii) demonstrate through the global oceanic distribution of desaturase genes the key role of these enzymes involved in the modulation of membrane fluidity for the colonization of different thermal niches by distinct Synechococcus lineages [START_REF] Breton | Unveiling membrane thermoregulation strategies in marine picocyanobacteria[END_REF]. We envision that Cyanorak will become a reference genome database for the taxonomic and functional annotation of not only newly released genomes and transcriptomes of marine picocyanobacteria, but also the everincreasing marine meta-omes, which given the natural abundance and ubiquity of these microorganisms in the marine environment constitute a significant part of all reads retrieved from the upper lit layer of marine waters. This paper is dedicated to the memory of our esteemed colleague Christophe Caron who was instrumental in launching the Cyanorak v2.1 project. We warmly thank Alexis Dufresne, who designed the first version (v1) of the database as well as Michelle G. Giglio and the Institute of Genome Science (IGS) staff for performing the initial automatic annotation of 32 Synechococcus and Cyanobium genomes using the IGS Manatee pipeline. We also thank Justine Pittera, Théophile Grébert, Garance Monier and Théo Sciandra for participating in the curation of the Cyanorak v2.1 database, the Roscoff Culture Collection and Sophie Mazard for maintaining and isolating some of the Synechococcus strains used in this study as well as the ABiMS platform for providing computational support for this work.

Figure 1 .

 1 Figure 1. Maximum likelihood tree based on 579 core proteins showing the

Figure 2 .

 2 Figure 2. Map of the isolation sites of the different sequenced strains included in the

Figure 3 .

 3 Figure 3. Genomic context of the narB gene encoding the nitrate reductase. A, genes

Figure 4 .

 4 Figure 4. An example of genome visualization using the JBrowse plugin of Cyanorak

Figure S3 :

 S3 Figure S3: Example of the genomic context of the malQ gene encoding the 4-alpha-glucanotransferase. This example shows that Synechococcus strains possess either cvrA or dvr upstream the malQ gene, while Prochlorococcus strains possess neither of these genes (see text for explanations).

Microbiol., 14, 372-386.

ACKNOWLEDGMENTS

FUNDING

This work was supported by the French "Agence Nationale de la Recherche" Programs SAMOSA (ANR-13-ADAP-0010), CINNAMON (ANR-17-CE2-0014-01) and IFB (ANR-11-INBS-0013), the Genoscope project METASYN, the Natural Environment Research Council grant NE/I00985X/1 and the European Union's Seventh Framework Programs FP7 MicroB3 (Grant 287589) and MaCuMBA (Grant 311975).

AVAILABILITY

The Cyanorak v2.1 information system is available at http://www.sb-roscoff.fr/cyanorak.

Supplementary Data are available at NAR online.

CONFLICT OF INTEREST

Authors declare no conflict of interest. Note that this D1 isoform is absent from all Prochlorococcus strains, while it can be present in up to 6 copies in Synechococcus/Cyanobium strains.


Moundir Dandani
email: amoundir.dandani@gmail.com

Abderrahmane Ghezal
email: babdghezal@yahoo.fr

Ala Bouhanguel
email: cbouhanguel@univ-corse.fr

Valérie Lepiller
email: dvalerie.lepiller@univ-fcomte.fr

Philippe Désévaux
email: ephilippe.desevaux@univ-fcomte.fr

Car

P Desevaux

Caractérisation du mélange dans un éjecteur supersonique destiné à la réfrigération solaire

Keywords: Ejecteur supersonique, mélange, CFD, réfrigération solaire

Introduction

L'utilisation de l'énergie solaire peut s'avérer un moyen intéressant pour produire du froid par le biais d'un cycle thermodynamique tritherme. Plusieurs technologies sont possibles pour mettre en oeuvre un tel cycle, notamment la technique de réfrigération par éjecto-compression [START_REF] Chunnanond | Ejectors. Applications in refrigeration technology[END_REF][START_REF] Paridasawas | Solar-Driven refrigeration systems with focus on the ejector cycle[END_REF][START_REF] Nedjar | La réfrigération solaire par cycle à éjecteur[END_REF]. Fig. 1. Principe de la réfrigération solaire par éjecto-compression Une installation de réfrigération solaire par éjecteur (Fig. 1) est constituée de deux circuits de fluide. Le premier cycle fluide récupère l'énergie solaire pour assurer la production de vapeur d'un second fluide à l'aide d'un générateur ou bouilleur (collecteur solaire). Ce second fluide sert à la production de froid au niveau de l'évaporateur. Dans un tel dispositif, l'éjecteur remplace le compresseur mécanique d'un système conventionnel. L'énergie fournie au éjecteur provient de la vapeur générée par le bais de l'énergie solaire. L'élément clef d'un tel système est l'éjecteur supersonique. Un des critères de performance des éjecteurs porte sur leur capacité à mélanger rapidement les flux moteur et induit. La littérature sur les éjecteurs propose un certain nombre d'études traitant de l'amélioration du processus de mélange soit par des méthodes passives [START_REF] Charyulu | Experimental study on mixing enhancement in two dimensional supersonic flow[END_REF][START_REF] Hari | Effectiveness of secondary tabs for supersonic mixing[END_REF], soit par des méthodes actives [START_REF] Murakami | Experiments on mixing enhancement in dual steam jets[END_REF][START_REF] Hidetaka | Control of pseudo-shock by slot injection[END_REF]. Toutefois, la capacité de mélange d'un éjecteur reste une propriété difficilement quantifiable. La simple observation de grandeurs classiques telles que pressions et débits s'avère insuffisante et l'analyse de ce processus repose souvent sur la visualisation qualitative de l'écoulement [START_REF] Desevaux | A method for visualizing the mixing zone between two co-axial flows in an ejector[END_REF][START_REF] Rao | Visualization and image processing of compressible flow in a supersonic gaseous ejector[END_REF]. L'obtention d'informations quantitatives sur le mélange nécessite alors une analyse plus détaillée de l'écoulement dans l'éjecteur. La CFD peut s'avérer être un outil précieux dans ce domaine. En effet, outre la possibilité de visualiser numériquement l'écoulement, la simulation CFD permet également de suivre l'´evolution du profil radial de la vitesse le long de la chambre de mélange de l'éjecteur [START_REF] Al-Doori | Investigation of refrigeration system steam ejector performance through experiments and computational simulations[END_REF]. L'analyse des profils de vitesse et notamment de leurs éventuelles discontinuités donne des informations sur l'interaction entre les deux écoulements et sur leur mélange. L'objectif de cette étude concerne le développement d'outils numériques permettant d'analyser le processus de mélange entre les jets primaire et induit et de quantifier la qualité du mélange. L'approche scientifique repose essentiellement sur des simulations CFD de l'écoulement dans un éjecteur air / air, 2D axisymétrique, en prenant en compte la turbulence par des modèles RANS. Après une validation des simulations s'appuyant sur des données expérimentales recueillies sur banc d'essai, deux approches permettant d'analyser numériquement la qualité du mélange dans l'éjecteur sont comparées. La première approche consiste à suivre l'évolution des distributions radiales de la vitesse le long de la chambre de mélange de l'éjecteur. La seconde repose sur l'observation du développement dans les zones d'interaction entre les flux primaire et secondaire.

Modèle CFD

Configuration de l'éjecteur étudié

L'éjecteur considéré dans cette étude est constitué de deux tuyères coaxiales (Fig. 2). Un compresseur à vis délivrant une pression maximale de 6 bar alimente la tuyère primaire qui détend l'air et l'accélère à une vitesse supersonique à sa sortie (Mach = 2,3), ce qui permet l'aspiration du flux secondaire à travers trois entrées disposées à 120° au tour de la chambre de tranquilisation.

Fig. 2. Schéma de l'éjecteur

Les deux flux d'air primaire et secondaire se mélangent ensuite dans la chambre de mélange en subissant un processus de recompression plus ou moins complexe et dépendant entre autre de la pression génératrice primaire et la géométrie de l'éjecteur. Le mélange est ensuite refoulé par le diffuseur dans le milieu atmosphérique. Le rapport géométrique A, correspondant au rapport de la section radiale de la chambre de mélange à la section au col de la tuyère primaire, est égal à 9. La longueur de la chambre de mélange est égale à 240 mm.

Conditions de simulation numérique

Les simulations sont réalisées à l'aide du code CFD Ansys-Fluent. Compte tenu de la géométrie de l'éjecteur, le domaine d'étude est considéré pour cette étude comme 2D axisymétrique (Fig. 3). Une condition au limite de type pressure-inlet est imposée à l'entrée de la tuyère primaire. Au niveau l'aspiration du flux secondaire, une section annulaire équivalente accompagnée d'une condition de type mass-flow inlet est utilisée pour cette étude. La valeur de débit imposée est celle mesurée expérimentalement sur le banc d'essai. Une condition de type pressure-outlet est fixée à la sortie du diffuseur correspondant à un refoulement à la pression atmosphérique. Les parois de l'éjecteur sont considérées comme adiabatiques. Le maillage utilisé, de type structuré, est composé d'environ 110000 éléments. Les équations Navier-Stokes sont résolues à l'aide du solveur pressure-based, avec couplage pression-vitesse et selon un schéma de discrétisation au second ordre. La turbulence de l'écoulement est prise en compte par trois modèles RANS : le modèle k-epsilon standard et les modèles k-omega standard et k-omega SST particulièrement bien adaptés aux écoulements compressibles de type jets circulaires avec cisaillement [START_REF] Wilcox | Turbulence modeling for CFD[END_REF].

Validation des simulations

La validation des simulations CFD est réalisée en comparant les distributions axiales de la pression statique obtenues numériquement avec différents modèles de turbulence et expérimentalement sur banc d'essai. Les mesures expérimentales ont été réalisées en utilisant une sonde d'exploration de la pression spécifiquement conçue à cet effet [START_REF] Bouhanguel | Etude numérique et expérimentale de l'interaction entre deux écoulements compressibles dans un éjecteur supersonique[END_REF]. Une comparaison pour deux valeurs de la pression génératrice primaire P 1 (3 et 4 bar), est présentée sur la figure 4. Pour ces deux valeurs de pression relativement faible et compte tenu du rapport géométrique A = 9 de l'éjecteur étudié, l'écoulement est caractérisé par la formation d'un train de chocs obliques en sortie de tuyère primaire, qui s'atténue ensuite dans la chambre de mélange. L'éjecteur fonctionne alors en régime mixte, c'est-à-dire avec un flux primaire supersonique en sortie de tuyère motrice et un flux secondaire qui reste quant à lui subsonique. La figure 4 montre un bon accord entre les résultats numériques et les mesures. C'est le modèle kepsilon standard qui donne les résultats les plus proches de l'expérimentation, notamment en ce qui concerne le nombre de chocs obliques et leur intensité. Fig. 4. Distribution axiale de la pression pour deux valeurs de la pression génératrice primaire.

Caractérisation du mélange

Evolution de la distribution radiale de la vitesse le long de l'éjecteur

La première approche considérée pour examiner le processus de mélange au sein de l'éjecteur consiste à comparer les distributions radiales de la vitesse obtenues numériquement. Les trois graphes présentés sur la Fig. 5 correspondent respectivement à des pressions génératrices primaires de 3, 4 et 5 bar. Les profils de vitesse couvrent toute la section de la chambre de mélange de diamètre 24 mm. Les positions A, B, C, D et E correspondent respectivement aux abscisses de 40, 70, 200, 308 et 538 mm le long de la chambre de mélange. On rappelle que l'abscisse de 40 mm correspond à la sortie de la tuyère primaire, l'abscisse de 70 mm à l'entrée de la chambre de mélange, l'abscisse de 308 mm à sa sortie et enfin que l'abscisse de 538 mm correspond à la section de sortie de l'éjecteur. Pour la pression génératrice P 1 = 3 bar, le profil radial en sortie de tuyère motrice (section A) est non uniforme. La vitesse est maximale (de l'ordre de 399 m/s) au coeur de l'écoulement. Elle correspond au jet primaire débouchant de la tuyère motrice. Le flux induit en périphérie de ce jet est caractérisé par une vitesse faible n'excédant pas la valeur de 9 m/s. Il est à noter l'existence au niveau de la section A de singularités sur la distribution de vitesse près de l'axe de l'éjecteur, qui sont sans doute dues à la présence d'un choc oblique. Au fur et à mesure que l'écoulement progresse dans la chambre de mélange, le profil de vitesse tend à s'homogénéiser lorsque le mélange entre les flux primaire et secondaire s'opère. La distribution radiale de la vitesse est uniforme à la sortie de cette chambre correspondant à l'abscisse D, ce qui indique que le mélange est complet entre les deux flux. Le diffuseur décélère ensuite ce mélange qui est refoulé à une vitesse d'environ 35 m/s. Le profil de vitesse obtenu dans la section D montre que le mélange est complètement réalisé à la sortie de la chambre de mélange. Les résultats obtenus en augmentant la pression génératrice primaire à 4 puis 5 bar confirment ces observations. La valeur de la vitesse du flux induit continue à augmenter régulièrement. Par contre, la vitesse du jet primaire en sortie de tuyère motrice tend à se stabiliser à une valeur proche de 568 m/s, correspondant à la valeur du nombre de Mach de 2,3 pour lequel est dimensionnée la tuyère motrice. Pour toutes les pressions primaires testées, le mélange des flux primaire et secondaire semble être totalement réalisé à la sortie de la chambre de mélange. Cette chambre remplit donc parfaitement son rôle. Le diffuseur se charge ensuite de décélérer le mélange avant son refoulement à l'atmosphère. Il apparaît de cette première analyse que l'évolution de la distribution radiale de la vitesse peut donner des informations sur le processus de mélange dans l'éjecteur.

Evolution de l'énergie cinétique turbulente le long de la chambre de mélange

L'interaction du jet supersonique avec le flux secondaire qui est entraîné avec une vitesse plus faible crée une couche limite entre les deux écoulements. Cette couche limite appelée couche limite de mélange est caractérisée par un fort cisaillement. Ce cisaillement délimite les zones non mélangées des zones mélangées. Ce cisaillement étant le siège de forte production d'énergie cinétique de turbulence k, nous avons donc suivi l'évolution de cette énergie le long de la chambre de mélange de l'éjecteur. Les résultats présentés sur la Fig. 6 concernent trois valeurs de la pression génératrice (3, 4 et 5 bar). Les positions A, B, C, D et E correspondent respectivement aux abscisses de 40 mm indiquant la sortie de tuyère motrice, de 70 mm indiquant l'entrée de la chambre de mélange, de 150 et 200 indiquant l'intérieur de la chambre de mélange et de 308 mm indiquant la sortie de la chambre de mélange cylindrique. Les résultats obtenus pour les trois valeurs de la pression P 1 considérées sont comparables. Ils mettent tous en évidence un profil radial de l'énergie cinétique turbulente à double lobes en sortie de tuyère motrice notamment. Ces maximums d'énergie, qui augmentent avec la pression P 1 , correspondent aux zones de cisaillement entre les flux moteur et induit. Dans la section A, l'énergie cinétique turbulente est nettement plus faible et homogène sur l'axe de l'éjecteur et en périphérie de tube de mélange. Ces deux régions correspondent respectivement au jet primaire et au flux secondaire qui ne subissent pas d'interaction entre eux. Dans la section B confondue avec l'entrée de la chambre de mélange cylindrique, ces zones à faible énergie turbulente commencent à se réduire au profit de la zone d'interaction entre les deux flux qui s'élargit au fur et à mesure que l'écoulement progresse dans la chambre de mélange. Les profils relatifs aux sections C et D confirment l'élargissement de cette zone d'interaction. Pour la pression P 1 de 3 bar, la distribution de l'énergie turbulente présente une forme quasi parabolique. Les profils relatifs aux pressions plus élevées (P 1 = 4 et 5 bar) conservent encore leur forme en double lobes. Cependant, l'ensemble des résultats à cette section montre que la production de l'énergie turbulente s'est très nettement accrue au coeur de l'écoulement. Enfin, les résultats obtenus à l'extrémité de la chambre de mélange correspondant à la section E montrent des distributions radiales de l'énergie de turbulence sensiblement uniformes et de faible intensité. Cela prouve que le cisaillement entre les deux flux a presque disparu et semble indiquer que le mélange est presque achevé. La Fig. 7 montre une comparaison du champ de l'énergie cinétique turbulente avec une visualisation expérimentale de l'écoulement, dans le cas d'une pression génératrice primaire de 4 bar. La visualisation expérimentale présentée ici a été réalisée sur le banc d'essai du laboratoire au cours d'une étude précédente [START_REF] Desevaux | Flow visualization methods for investigating an induced flow ejector[END_REF]. Elle a été obtenue par tomographie laser en introduisant des traceurs dépolarisants dans le flux induit. La région d'écoulement marquée par ces traceurs diffusants apparait donc en clair sur la photographie. Par contre, la zone centrale qui apparait en sombre, correspond à la portion de flux primaire qui ne s'est pas mélangée avec le flux induit. La longueur de cette zone d'écoulement représente donc la longueur nécessaire au mélange complet entre les deux flux. En comparant cette image avec le champ d'énergie cinétique turbulente obtenu par CFD, on constate un bon accord visuel entre cette zone sans mélange et la région (de couleur bleue) caractérisée par une faible valeur de k. La corrélation entre zone sans mélange et zone à faible valeur d'énergie cinétique turbulente semble se confirmer. La Fig. 8 présente l'évolution de l'énergie cinétique turbulente le long de l'axe de l'éjecteur. Cette distribution, obtenue numériquement, est relative à une pression génératrice primaire P 1 = 5 bar. Elle montre une zone d'écoulement située en sortie de tuyère primaire où la production d'énergie turbulente reste faible. Cette zone est donc à rapprocher de la zone sans mélange visualisée expérimentalement. Lorsque les deux flux interagissent en se mélangeant, cela se traduit par une augmentation de l'énergie turbulente. Cette augmentation est clairement visible à partir de l'abscisse de 130 mm. L'énergie turbulente est alors multipliée par un facteur 4 sur une distance d'écoulement de 20 mm.

Conclusion

Bien que la présente étude est menée sur un éjecteur supersonique à air /air, les méthodes proposées pour l'évaluation de la qualité du mélange sont toutefois applicables à d'autres gaz ce qui permet à terme de mener des études relatives à l'amélioration du processus de mélange dans les éjecteurs. Cette étude, basée sur une modélisation 2D axisymétrique de l'écoulement, a montré que l'analyse de l'évolution des distributions radiales de la vitesse et de l'énergie cinétique turbulente le long de l'éjecteur peut fournir des informations sur le processus de mélange entre les flux primaire et secondaire. Les différents résultats numériques obtenus présentent entre eux une bonne cohérence. Ils montrent que le mélange est complément réalisé à l'entrée du diffuseur, confirmant ainsi que la chambre de mélange rempli parfaitement son rôle. Par ailleurs, l'évolution de l'énergie cinétique turbulente semble fournir des informations correctes sur la zone sans mélange. Les résultats obtenus en comparant les champs de l'énergie cinétique turbulente aux visualisations expérimentales sont en effet en bon accord. Toutefois, il semble difficile de pouvoir conclure définitivement quant à la fiabilité de ces critères pour caractériser le mélange. Une analyse plus poussée s'appuyant en particulier sur des résultats expérimentaux est donc nécessaire pour pouvoir conclure quant au critère le plus judicieux pour caractériser le mélange dans l'éjecteur.

Fig. 3 .

 3 Fig. 3. Domaine d'étude et conditions aux limites

Fig. 5 .Fig. 6 .Fig. 7 .

 567 Fig. 5. Evolution des distributions radiales de la vitesse le long de la chambre de mélange pour différentes pressions P1

Fig. 8 .

 8 Fig. 8. Distribution axiale de l'énergie cinétique turbulente (P 1 = 5 bar).


Ala Bouhanguel
email: bouhanguel@univ-corse.fr

Valérie Lepiller
email: valerie.lepiller@univ-fcomte.fr

Philippe Désévaux
email: philippe.desevaux@univ-fcomte.fr

Moundir Dandani
email: moundir.dandani@gmail.come.lmfta

Abderrahmane Ghezal
email: abdghezal@yahoo.fr

Vi

P Desevaux

Visualisations expérimentales et numériques des instabilités dans un éjecteur air -air supersonique

Keywords: Ejecteur, Supersonique, Instabilités, Laser tomography, CFD 1

teaching and research institutions in France or abroad, or from public or private research centers.

Introduction

Les éjecteurs sont des appareils que l'on rencontre dans de nombreuses applications (aéronautique, génie des procédés, réfrigération solaire, vide, ..). Ces appareils sont constitués en général de deux tuyères coaxiales. Le jet supersonique délivré par la tuyère primaire crée une dépression dans la seconde tuyère qui peut être mise a profit pour créer le vide (fonctionnement sans flux induit) ou aspirer et entrainer un flux induit (fonctionnement avec flux induit). L'interaction entre les deux flux est complexe et met en oeuvre de nombreux processus complexes (chocs, turbulence, mélange, voire condensation). La majorité des études sur ces appareils sont des analyses globales destinées à caractériser les performances de ces systèmes. Les analyses locales, plus rares, permettant une analyse plus fine des phénomènes mis en jeu dans l'écoulement. La visualisation de l'écoulement, par des techniques expérimentales ou numériques, permet d'obtenir de précieuses informations quant au processus de recompression par chocs [START_REF] Desevaux | Visualization of secondary flow choking phenomena in a supersonic air ejector[END_REF], de mélange [START_REF] Yang | Numerical investigation on the mixing process in a steam ejector with different nozzle structures[END_REF], de condensation [START_REF] Marynowski | Experimental and numerical visualizations of condensation process in a supersonic ejector[END_REF] et s'avère très utile pour la validation de simulations numériques [START_REF] Desevaux | On the use of laser tomography techniques for validating CFD simulations of the flow in supersonic ejectors[END_REF]. Toutefois, ces visualisations sont souvent obtenues avec des éclairages longs ou par des simulations en stationnaire ce qui masque les éventuelles instabilités de l'écoulement. Ces instabilités, qui peuvent jouer un rôle prépondérant sur les performances de l'éjecteur, notamment sur sa capacité de mélange [START_REF] Murakami | Experiments on Mixing Enhancement in Dual-Stream Jets[END_REF]. L'objectif de ce papier est de montrer que ces instabilités peuvent être détectées et examinées grâce à l'utilisation d'un éclairage pulsé pour les visualisations expérimentales de l'écoulement et par le développement d'un modèle CFD 3D instationnaire avec modélisation des grande échelles de turbulence (LES).

Conditions d'expérimentation

L'éjecteur est constitué de deux tuyères convergentes-divergentes coaxiales (figure 1). La tuyère primaire est alimentée par de l'air à une pression génératrice P

1 .FIG. 2 -

 12 FIG. 1 -Géométrie de l'éjecteur étudiéLa visualisation de l'écoulement dans la chambre de mélange est obtenue par tomographie laser pulsé. La source lumineuse utilisée est un laser Nd-YAG double en fréquence (532 nm) émettant des pulses laser de 15 ns et de 100 mJ. L'écoulement est illuminé par une nappe de lumière remontant l'écoulement. L'observation se fait perpendiculairement à l'axe de l'éjecteur au moyen d'une caméra CCD synchronisée au laser. La simulation numérique est menée sur le code CFD ANSYS Fluent. Le maillage du domaine comprend 4 millions d'éléments. Le pas de temps varie entre 0,10 s et 1 ms afin d'évaluer l'influence de ce paramètre temporel sur la détection des instabilités. Des conditions de pression sont imposées aux entrées et à la sortie de l'éjecteur. La turbulence de l'écoulement est modélisée par l'approche LES. Le schéma de discrétisation utilisé est du type Bounded Central Differencing, avec une discrétisation spatiale du 3 ème ordre. Le filtrage est obtenu par le modèle de Smagorinsky-Lilly. Le niveau de résolution est également fortement lié à la finesse du maillage. La grille de maillage utilisée est constituée d'éléments volumiques compris entre 2,2.10 -9 et 4,5.10 -8 m 3 . .

RésultatsLa figure 2 présente des visualisations de l'écoulement dans la chambre de mélange (sur environ 200 mm après la section de sortie de la tuyère motrice) obtenues lorsque l'éjecteur fonctionne en régime mixte. Ce régime est caractérisé par la présence d'un jet supersonique en sortie de tuyère motrice et par un flux induit qui reste subsonique dans la tuyère secondaire. La figure 2a montre une