Karine Alix
email: karine.alix@agroparistech.fr

Pierre R Gérard

Trude Schwarzacher

ON POLYPLOIDY IN ECOLOGY AND EVOLUTION REVIEW Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants

Keywords: Polyploidy, hybrids, ecology, adaptation, evolution, genomics, chromosomes, speciation, whole genome duplication (WGD), crops, weeds, phylogeny, bryophytes, angiosperms

 Background. Polyploidy or whole genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridisation events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this article, consider genomic aspects of polyploidy.

 Approaches. Discovery of the evolutionary consequences of new, evolutionarily recent, and ancient polyploidy requires a range of approaches. Large scale studies of both single species, and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes,

showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution, require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.

 Conclusions: The success of polyploidy, driving out the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidisation events. Strikingly, polyploidisation often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting that concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole genome duplication act as a driver of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

INTRODUCTION

About half of all higher plant species are recognizable as evolutionarily recent polyploids, where multiple whole genomes or sets of chromosomes have come together from close ancestors [START_REF] Soltis | Polyploidy and genome evolution in plants[END_REF]. Additionally, over evolutionary time, all flowering plants have at least one polyploidy event, also known as a whole genome duplication (WGD), in their ancestry, from before the divergence of gymnosperms and angiosperms, the ζ (zeta) event (see Fig. 1 and references therein). Angiosperms, including Amborella and the basal angiosperms (i.e. ANA, for Amborellales, Nymphaeales, Austrobaileyales) that are sisters to all the other angiosperms, have a second polyploidy event in their lineage (ε, epsilon;Amborella Genome Project, 2013). Analyses of whole genome sequences in the last decade have identified additional, and often multiple, polyploidy events in the ancestry of every eudicot and monocot where the genomes have been sequenced (summarized in Fig. 1). Notably, the near-universal occurrence of multiple polyploidy events [START_REF] Wendel | The wondrous cycles of polyploidy in plants[END_REF] during plant evolution is in contrast to most groups of animals in both recent and long-term evolutionary history (e.g. [START_REF] Hoffmann | Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates[END_REF], marking a significant divergence between evolutionary mechanisms in the two kingdoms.

With respect to its omnipresence along the evolutionary history of higher plants, polyploidy has been the subject of numerous reviews with emphasis on the genetic and genomic consequences of WGDs [START_REF] Soltis | Polyploidy: Pitfalls and paths to a paradigm[END_REF]. The present article has two main objectives: firstly, overviewing the papers in this Special Issue "Polyploidy in Ecology and Evolution", and secondly to discuss complementary polyploidy-related topics covered. In the Issue, we made the choice to consider not simply the occurrence of polyploidy (or WGD) in plants (including the bryophyte Sphagnum), but also provide an overview of the consequences of polyploidy in adaptation, speciation and evolution in plants: the relationships between polyploidy and stressful environmental conditions have suggested a major role of polyploidy in adaptation. This has been extensively analysed for cultivated plants, and we review this topic, in the context of concepts related to papers in the Special Issue, many of which present research in the novel area of polyploidy in natural plant populations. With the number of polyploidy events being revealed in plant evolution, the study of its evolutionary significance on wild plant species at the population scale, considering both evolutionarily ancient (deep) phylogenies and recent polyploids (some below the level of species), is now underway. The Special Issue articles consider the success and diversity found in polyploids from the ecological and evolutionary points of view, including developmental and genetic studies. Several papers deal with the relationships of polyploidy with plant reticulate evolution (i.e. natural hybridisation), while others bear on the origin and formation of neopolyploids. Some papers discuss the relationships between allopolyploidy and reproductive systems, two major processes driving angiosperm diversification, and other papers highlight the link between polyploidy and adaptation, in a biogeographical context. Finally, a review dedicated to the impact of transposable elements on polyploidy plant genomes gives consideration to the molecular basis of genomic conflicts, particularly present in genome duplications with hybrid origins. We have specifically developed this renewed interest for the study of polyploidy in plants with new avenues of investigations dedicated to the epigenetic consequences of polyploidy and their role for plasticity and adaptation in plants.

OCCURRENCE AND DETECTION OF POLYPLOIDY IN PLANTS

Plant evolution and polyploidy

Since the historical Greek and Roman cultures, more than two millennia of research on plant diversity and relationships have established a robust phylogeny, placing all plants in a few monophyletic groups (as exemplified with angiosperms that constitute now a single monophyletic group), most recently based on evidence from DNA sequences [START_REF] Apg Iv | An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV[END_REF].

Novel interpretations and new discoveries in the fossil record have been important for identifying innovations and divergences within plants (e.g. [START_REF] Matsunaga | Root evolution at the base of the lycophyte clade: insights from an Early Devonian lycophyte[END_REF]Gondolfo and Hemsen, 2017) giving extra strength to modern phylogenies. Polyploidy is a confounding factor in phylogenetic analysis, in particular when it involves interspecific hybridisation at the origins of the genome duplication. The resulting duplicated gene copies may lead to incongruence among multiple gene phylogenies, and the reticulate evolutionary patterns that mean lineages -typically at the level of genus or tribe and below -will be defined as multiple monophyletic groups (e.g. [START_REF] Fortune | Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)[END_REF]. Understanding the evolutionary and biological processes in their past diversification and considering future evolutionary pathways is a major research objective, notably addressed in the articles presented here.

Polyploidy and genome rearrangements, complementing mutation and recombination, are major evolutionary events, having the potential to lead to genetic and reproductive isolation.

Most of the nodes within the phylogeny of plants (Fig. 1) represent disruptive changes in evolution, with vasculation, seeds and flowers representing successive evolutionary innovations. Previous Special Issues of Annals of Botany have stressed the major role of pollination biology and co-evolution with pollinators in the ecological diversification of flowering plants (e.g. [START_REF] Van Der Niet | Pollinator-driven ecological speciation in plants: new evidence and future perspectives[END_REF][START_REF] Friis | Cretaceous angiosperm flowers: Innovation and evolution in plant reproduction[END_REF]. Another important feature of angiosperms is their broad metabolic performance and their remarkable photosynthetic efficiencies based on carbon-and water-use capacities, thanks to morphological innovations in leaves, wood and roots, which have enabled colonizing a large diversity of habitats [START_REF] Field | The ecophysiology of early angiosperms[END_REF]. Angiosperm diversity can also be linked to the impact of the rounds of polyploidy (WGD) duplicating all the genes [START_REF] Tank | Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications[END_REF]. As well as potentially giving reproductive isolation, polyploidy leads to multiplying the number of genes and incorporating redundancy in function, enabling new genetic variability that may be acted upon by natural selection for evolution and adaptation. Indeed, allopolyploidy (associated with interspecific hybridisation, see below) has long been considered as a source of the "most important amendment to Darwin and Wallace's account of evolution" [START_REF] Haldane | The theory of natural selection to-day[END_REF].

Detection of polyploidy

Extant polyploid plants can be detected by counting chromosome numbers in cytological metaphase preparations made from a group of related accessions (or species, as shown in Fig. 2). Where chromosome numbers in related plants are multiples (or sums) of others, the plant is likely to be a recent polyploid, and many species have a ploidy series with a base chromosome number x, including diploids 2x and polyploids such as triploids 3x, tetraploids 4x and polyploids with even higher ploidies (see [START_REF] Heslop-Harrison | Polyploidy. Reference Module in Life Sciences (LIFE)[END_REF]. Equally, DNA content of the accessions can be measured by flow cytometry or Feulgen densitometry, and will show an additive series from the ancestral diploids to multiples in the polyploids [START_REF] Kron | Applications of flow cytometry to evolutionary and population biology[END_REF]. Nevertheless, DNA content and chromosome number are not always directly correlated to ploidy levels. For instance, karyotype evolution by chromosome fission and fusion has significantly marked the evolutionary history of diverse plant lineages, making thus difficult to infer ploidy levels from cytogenetic data (e.g. in Crocus - [START_REF] Harpke | Phylogeny, karyotype evolution and taxonomy of Crocus series Verni (Iridaceae)[END_REF]. Where species have diverged before coming together in a polyploid, the use of total genomic DNA as a probe for in situ hybridisation has been valuable to both identify the occurrence of a polyploid, and assist with identification of the ancestral species (e.g. [START_REF] Hunt | Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum[END_REF][START_REF] Patel | Somatic hybrid plants of Nicotiana × sanderae (+) N. debneyi with fungal resistance to Peronospora tabacina[END_REF].

Within many species and species complexes, polyploid series can be present and are described as cytotypes (in this Special Issue e.g. [START_REF] Čertner | Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids[END_REF][START_REF] Paule | Ecological range shift in the polyploid members of the South American genus Fosterella (Bromeliaceae)[END_REF] or see [START_REF] Taketa | Comparative physical mapping of the 5S and 18S-25S rDNA in nine wild Hordeum species and cytotypes[END_REF] or when polyploidy events are older, as different species (Hordeum; [START_REF] Cuadrado | On the allopolyploid origin and genome structure of the closely related species Hordeum secalinum and Hordeum capense inferred by molecular karyotyping[END_REF].

Two main types of recent polyploidy can be distinguished. Autopolyploidy defines duplication of one genome within one species, which results in homologous chromosome sets in the cell (a genome is normally designated by a capital letter; thus the diploid AA doubles to become the autotetraploid AAAA). Allopolyploidy defines WGD associated with the merger of two or more divergent genomes in a single nucleus following interspecific hybridisation, resulting in homoeologous chromosome sets in the cell (AA×BBAABB). In practice, autoand allopolyploidy are not entirely separate, since this terminology depends on the taxonomic definition of a species and the scope of a designated 'genome'. Higher polyploids may be combinations as results of their evolutionary histories that have been marked by recurrent WGDs including both auto-and allopolyploidy events, thus giving the 'auto-allo-polyploid' designation (usually summarized as polyploid). For ancient WGD events, where the ancestral diploid species (singular or plural) are unknown and DNA sequences are diverged, auto-or allopolyploidy, as depicted in Figure 1, cannot be distinguished.

For the detection of ancient polyploid events, whole genome sequencing coupled with comparative genomics has proved to be remarkably efficient; this is particularly well illustrated by the Amborella genome project (2013). Typically, following assembly of the DNA sequence, all-frame protein translations are made to produce a full set of gene predictions. Structural comparisons on the set of gene predictions then allow the identification of paralogous gene pairs used to reconstruct ancient WGDs. Indeed, even over very long evolutionary periods, regions of synteny -the same list and order of genes -and of similar, paralogous genes (thus corresponding to syntenic blocks) are readily identified on different chromosomes, enabling the detection of multiple ancient whole genome duplication events (see Fig. 1 and its references).

HOW SUCCESSFUL ARE POLYPLOIDS? About the evolutionary success of polyploidy Before the recognition of the ubiquitous ancient polyploidy or whole genome duplication events in plants, polyploids were widely considered as being present in many lineages. The long-term compared to short-term evolutionary success of polyploids, whether in crops or wild species, was a significant question [START_REF] Soltis | Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al[END_REF][START_REF] Arrigo | Rarely successful polyploids and their legacy in plant genomes[END_REF]. [START_REF] Mayrose | Recently formed polyploid plants diversify at lower rates[END_REF] consider that "polyploidy is most often an evolutionary dead end" with respect to neopolyploids and their associated low diversification, and thus speciation rates, in comparison to diploids. Nevertheless, polyploids do represent longer-term evolutionary successes; the WGD events at their origins may have generated the necessary genetic diversity that has been under positive selection for long periods, and then associated with phenotypic novelty, adaptability and higher fitness. Of course, the role of subsequent genome evolution (mutation, chromosome rearrangement, transposable element mobilisation) in contributing to this genetic diversity has also to be considered. Interestingly, the polyploidy events that have marked the evolutionary history of the green plant lineage occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, suggesting a role of polyploidy in adaptive speciation [START_REF] Bodt | Genome duplication and the origin of angiosperms[END_REF]. This is particularly well illustrated with the survival and proliferation of polyploid plant lineages during the Cretaceous-Tertiary (K-T) mass extinction event [START_REF] Fawcett | Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event[END_REF]Fig. 1). The occurrence of polyploidy in response to stressful conditions has been notably analysed in the context of plant domestication that represents conditions of strong selection pressure for adaptation to human cultivation.

Polyploidy and plant domestication

Many crop species have been identified as polyploids through the presence of polyploid series in chromosome number (e.g. [START_REF] Sabath | Whole-genome duplication as a key factor in crop domestication[END_REF] and through generation of hybrids (e.g. [START_REF] Renny-Byfield | Doubling down on genomes: polyploidy and crop plants[END_REF], and many crops are relatively recent polyploids [START_REF] Leitch | Genomic plasticity and the diversity of polyploid plants[END_REF]. This has led to the hypothesis of some relationship between intensive selection, typically accompanying plant domestication, and polyploidy. [START_REF] Sabath | Whole-genome duplication as a key factor in crop domestication[END_REF] considered that polyploidy followed by domestication was a key feature in early selection of crops and showed that domesticated plants have gone through more polyploidy events than their wild relatives. Nevertheless, it can be noted that the advantages of polyploidy under domestication are not overwhelming: the top three crops in the world, all cereal grains, are wheat (a modern hexaploid 2n=6x=42; Fig. 2C), rice (diploid, 2n=2x=14), and maize (a paleotetraploid, 2n=4x=20). With the strict polyploid selection criteria of [START_REF] Sabath | Whole-genome duplication as a key factor in crop domestication[END_REF], 30% of crops were polyploid compared to 24% of wild species.

Induced or post-domestication polyploids represent a small proportion of crops (reviewed by [START_REF] Sattler | The polyploidy and its key role in plan breeding[END_REF]. As well as the genetic buffering and increased number of gene alleles associated with the increase in cell size, a major consequence of polyploidy may be the global increase size of the organs (including leaves, stems, flowers, stigmas, tubercles) of the polyploid compared to its diploid counterpart; it is thus generally considered that polyploidy may increase fruit size as well as seed size, valuable traits for crop breeding. Such a consequence also illustrates one of the major advantages of polyploids that is their 'doubled interspecific hybrid' composition, which directly results in fixing heterozygosity at the origin of heterosis, or hybrid vigour [START_REF] Comai | The advantages and disadvantages of being polyploid[END_REF]. [START_REF] Wu | Induced polyploidy dramatically increases the size and alters the shape of fruit in Actinidia chinensis[END_REF] stated that there has been little systematic evaluation of fruit from induced polyploids in comparison with diploids, and that there was only little evidence for larger fruits. However, their detailed work in kiwifruit (Actinidia chinensis) showed that colchicine-induced autotretraploids were some 50% larger than their diploid progenitors, and that the increase was stable during vegetative propagation.

In addition, specific work on wheat polyploids clearly demonstrated that seeds from synthetic hexaploid wheats were significantly larger than seeds from either progenitor, tetraploid or diploid [START_REF] Kenan-Eichler | Wheat hybridization and polyploidization results in deregulation of small RNAs[END_REF]. Thus, one can suggest that the consequences of polyploidy extend to developmental effects (see also [START_REF] Münzbergová | Consequences of polyploidization vary between populations and their estimate is affected by colchicine application even in the second generation[END_REF].

Further investigations of the consequences of genome duplication in relation with adaptation abilities in natural populations from various plant lineages should provide a valuable insight into the important evolutionary process of polyploidy, as reported by the articles presented in this Special Issue.

POLYPLOIDY IN ECOLOGY AND EVOLUTION

Polyploidy, diversity and reticulate evolution

Understanding the components of the evolutionary success of polyploidy has generated important research activity in the last twenty years. Autopolyploidy has received relatively little attention by evolutionary biologists, not least since diploids and autopolyploids can be considered as one species (sometimes subject to redefinition as, for example, in Brachypodium by [START_REF] Catalan | Evolution and taxonomic split of the model grass Brachypodium distachyon[END_REF]; indeed, it has been estimated that the evolutionary advantages of allopolyploidy are largely superior (Parisod et al., 2010b). Evolutionary advantages of allopolyploidy can be associated with merger of differentiated genomes (i.e. via interspecific hybridisation) with consequent genomic restructuring and rebalancing of gene expression, giving phenotypic changes (Parisod et al., 2010b;[START_REF] Hegarty | Genomic clues to the evolutionary success of polyploid plants[END_REF][START_REF] Tayalé | Natural pathways to polyploidy in plants and consequences for genome reorganization[END_REF][START_REF] Mutti | Evolution of gene expression balance among homeologs of natural polyploids. G3: Genes, Genomes[END_REF]. How large is the role of reticulate evolution in the evolutionary success of flowering plants (reviewed by [START_REF] Soltis | The role of hybridization in plant speciation[END_REF], and should polyploidy be considered, following interspecific hybridisation, as the major driver of plant evolution and speciation? Hybridisation has been proposed as a direct driver of WGD, but the causal relationships between both processes are far from clear, and autopolyploidisation has certainly contributed to plant diversification [START_REF] Soltis | Autopolyploidy in angiosperms: have we grossly underestimated the number of species?[END_REF][START_REF] Buggs | Does hybridization between divergent progenitors drive whole-genome duplication?[END_REF][START_REF] Barker | Spreading wine and flying high: the evolutionary importance of polyploidy after a century of study[END_REF].

Diploid plants, including hybrids, produce unreduced gametes at relatively high rates, which participate in the formation of many polyploid lineages [START_REF] Ramsey | Neopolyploidy in flowering plants[END_REF][START_REF] Otto | The evolutionary consequences of polyploidy[END_REF]. These lineages are often reproductively isolated from their progenitors, giving rise to new species or cultivars (Čertner et al., 2017 see below; and e.g. in Crocus, [START_REF] Orgaard | The hybrid origin of two cultivars of Crocus (Iridaceae) analysed by molecular cytogenetics including genomic Southern and in situ hybridization[END_REF], Alsayeid et al., 2015;in Mimulus, Sweigart et al., 2008;[START_REF] Vallejo-Marín | Speciation by genome duplication: repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus[END_REF].

Interploid fitness loss might not be universal though, because polyploid plant species with odd chromosome numbers are widespread [START_REF] Otto | The evolutionary consequences of polyploidy[END_REF] and triploids can often have a role of bridges between diploid and tetraploid species [START_REF] Ramsey | Pathways, mechanisms, and rates of polyploid formation in flowering plants[END_REF] often exploited in breeding [START_REF] Heslop-Harrison | Domestication, genomics and the future for banana[END_REF]. The role of hybridisation in creating high genetic variability by producing new genotypes at the onset of potential speciation events is a question that has been recurrently addressed, notably by two papers in this Special Issue.

In the first paper from [START_REF] Yan | Asymmetric natural hybridization varies among hybrid swarms between two diploid Rhododendron species[END_REF], the role of hybridisation in diversifying and structuring natural populations is particularly well illustrated within the genus Rhododendron, where interspecific hybridisation is frequent. By analysing twenty-four Rhododendron populations including fifteen independent hybrid swarms, the authors have addressed the question of the extent of hybridisation in population structure and differentiation [START_REF] Yan | Asymmetric natural hybridization varies among hybrid swarms between two diploid Rhododendron species[END_REF]. Using microsatellite and chloroplast DNA sequencing, the authors demonstrate that hybridisation events are complex and highly variable from one population to another, and result mainly in introgressions. The recurrent backcrosses lead to new allele combinations, generating genetic diversity for new variants among populations and potentially driving speciation.

Similarly, [START_REF] Landrein | Untangling the reticulate history of species complexes and horticultural breeds in Abelia (Caprifoliaceae)[END_REF] investigated the genetic diversity among five Abelia species (Caprifoliaceae) originating from China, by analyzing wild taxa and horticultural varieties, to identify the origins of the genetic diversity, including that exploited in breeding programmes.

Their study was based on phylogenetic reconstruction using nuclear and chloroplast markers and molecular genotyping for genetic diversity and population structure analysis. They demonstrate that the Abelia genus has been subjected to recurrent hybridisation and introgression, at the origins of allopatric speciation events. Their results demonstrate the value of exploiting hybridisation, which, in association with random recombination, may produce interesting allele combinations for ornamental breeding purposes.

A third paper of the Special Issue also reports the study of the relationships between interspecific hybridisation and genetic diversity, but includes the genome duplication process by analysing and comparing the allopolyploids. [START_REF] Cuadrado | On the allopolyploid origin and genome structure of the closely related species Hordeum secalinum and Hordeum capense inferred by molecular karyotyping[END_REF] demonstrate the role of allopolyploidy in diversifying Hordeum (a genus with nearly half of the taxa that are polyploids, and where some species such as Hordeum murinum are represented by morphologically indistinguishable diploid and autopolyploid cytotypes, [START_REF] Taketa | Comparative physical mapping of the 5S and 18S-25S rDNA in nine wild Hordeum species and cytotypes[END_REF], by analysing the hybrid genome composition of two closely related allotetraploid species using molecular cytogenetics. Even closely related genomes in the allopolyploid harbour high genomic diversity, enabling colonization of different geographical areas. The evolutionary divergence of H. secalinum and H. capense and their current intra-genome diversity may be thus related to the differential genomic and chromosomal modifications encountered by the two parental genomes that merged during the allopolyploidisation event.

Outside the flowering plants, polyploidy has been important in the evolution of mosses (Shaw et al., 2016 and Fig. 1), where it is associated to hermaphroditism [START_REF] Crawford | Correlated evolution of sexual system and life history traits in mosses[END_REF] and more generally to changes in mating systems [START_REF] Jesson | Polyploidy influences sexual system and mating patterns in the moss Atrichum undulatum sensu lato[END_REF]. With respect to the high level of fixed heterozygosity observed for numerous moss species, a preponderant role for allopolyploidy in bryophyte diversification has been suggested. This allopolyploidy-based evolutionary process is particularly exemplified in Sphagnum [START_REF] Ricca | Allopolyploidy and homoploid hybridization in the Sphagnum subsecundum complex (Sphagnaceae: Bryophyta)[END_REF], which is the model of the study reported in this Special Issue. [START_REF] Karlin | Allo-allo-triploid Sphagnum ×falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers[END_REF] investigated the allelic diversity of the peat moss Sphagnum ×falcatulum, a double allopolyploid species originating from the combination of three monoploid genomes from three ancestral species (i.e.

it is an allo-allo-triploid). They used SSR genotyping on a large sample of S. ×falcatulum gametophytes (in comparison to the immediate progenitors, i.e. the monoploid genomes) from different populations widespread in the Holantarctic. Most of the genetic diversity is captured directly from the three ancestral monoploid genomes, and multiple origins of S. ×falcatulum are likely (i.e. recurrent allopolyploidisation). Allopolyploidy may thus be the single most important factor in generating the genetic diversity allowing this peat moss to colonize the Holantarctic region so successfully.

Neopolyploid formation: a chromosomal point of view

Polyploids are usually formed from hybridisation of taxonomically close species, where the gene content, sequences and often chromosomal organisation, if not the repetitive DNA (e.g. Fig. 2), are similar. New hybrids in the first or early generations, including both spontaneous hybrids and those made in a research or plant breeding context, are classified as neopolyploids. In nature, some species complexes with high phenotypic diversity and many microspecies of various ploidies give complex taxonomic problems (e.g. Rhododendron discussed above; Taraxacum, [START_REF] Majeský | The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts[END_REF]Rubus, Heslop-Harrison, 1968). The taxonomic challenges and diversity in populations mean that studies with large numbers of individuals and molecular markers are required.

The first advantage of allopolyploids (AABB) in comparison to homoploid hybrids (AB) is the immediate recovering of homologous chromosome pairs as a prerequisite to regular meiosis, and therefore potentially restoring fertility (at least partial) in the resulting hybrid genotypes, thanks to chromosome set doubling. Nevertheless, polyploids usually require also a tight genetic control of crossing-over formation and distribution to minimize aneuploidy and to ensure further fertility and genome stability, and thus the establishment and success of neopolyploids [START_REF] Jenczewski | From diploids to allopolyploids: the emergence of efficient pairing control genes in plants[END_REF][START_REF] Grandont | Meiosis and its deviations in plants[END_REF]. Three papers in this Special Issue focus on neopolyploids, dealing with the extent of the formation of polyploid cytotypes in natural conditions, which mainly involve the production of unreduced gametes from diploids (as mentioned above) and the immediate consequences of polyploidisation that can be identified using synthetic polyploids.

In their analysis of a collection of more than 800 samples of dogroses (Rosa sect.

Caninae), [START_REF] Herklotz | Multiple and asymmetrical origin of polyploidy dog rose hybrids (Rosa L. sect. Caninae (DC.) Ser.) involving unreduced gametes[END_REF] addressed the question of the extent of natural interspecific hybridisation between the subsections Caninae and Rubigineae, finding populations had a mixture of hybridogenic and non-hybridogenic individuals. Dogroses comprise many allopolyploid species (4x, 5x, 6x) notably thanks to a unique asymmetric meiosis process with only two sets of chromosomes forming bivalents that results in haploid pollen grain but a polyploid egg cell [START_REF] Ritz | Microsatellite analyses of artificial and spontaneous dogrose hybrids reveal the hybridogenic origin of Rosa micrantha by the contribution of unreduced gametes[END_REF]. The authors demonstrate that polyploids are more frequent in Rubigineae hybrids in relation with their higher capacity in producing unreduced gametes than in Caninae, representing a major bias between reciprocal crosses. However, despite their viability and abundance, it seems that neopolyploid hybrids, in contrast to non-hybrids, do not spread between localities. In a large scale spatio-temporal study in central Europe, Čertner et al. (2017) used flow cytometry data on more than 11,000 individuals, as well as ex situ germination data, to study the cytotypic structure and dynamics of a contact zone between diploid and tetraploid populations of the annual herb Tripleurospermum inodorum (Asteraceae). In spite of an apparent substantial amount of gene flow between the two cytotypes, and the presence of fertile triploids that could serve as bridges to new polyploids (see above), alternative cytotypes are rare. Newly formed tetraploids were extremely rare and were thus not able to establish, suggesting that successful tetraploids probably result from one or a few rare and ancient polyploidisation events -echoing the theory developed by [START_REF] Mayrose | Recently formed polyploid plants diversify at lower rates[END_REF]. Together, these studies show the importance of mixed-ploidy populations in generation of cytotype variation, with population structure (in sympatry) that may help maintain a resource of genetic diversity conferring at least long-term adaptive advantages.

Neopolyploids, and in particular synthetic polyploids, are the most appropriate plant material to analyse and further understand the direct consequences of polyploidisation during speciation. [START_REF] Münzbergová | Consequences of polyploidization vary between populations and their estimate is affected by colchicine application even in the second generation[END_REF] addresses this question on the model Vicia cracca that comprises both diploid and autotetraploid cytotypes. By analyzing and comparing natural diploids, natural tetraploids and synthetic tetraploids from four different populations, the author demonstrates the direct impact of polyploidy on morphological traits (e.g. seed weight, plant height, stomata size). This study also highlights the necessity to analyse multiple populations of polyploids to provide robust conclusions about the impact of polyploidisation that may be variable with respect to the diversity of the populations at the origins of the new polyploids.

Finally, the author performed a comparative study between the synthetic tetraploids and their diploid offsprings to evaluate the impact of the colchicine treatment at the origin of the synthetic polyploids: only the analysis of the third and subsequent generations of synthetic polyploids may allow to reveal the consequences of polyploidisation per se. Such conclusions should be beneficial to the study of 'old' polyploid species (e.g. oilseed rape, cotton, wheat, tobacco) for which the true diploid progenitors are not available anymore and the synthetic polyploids are the unique plant material useful to model and understand their formation.

Polyploidy and reproductive systems

Reproduction, whether sexual, apomictic or vegetative, is central to the success of polyploids. Notably, the near-universal occurrence of multiple polyploidy events in plant evolution is in complete contrast to the animal kingdom in both recent and long-term evolutionary history, where most analyses have found only one or two early whole genome duplication events, such as the R1 and R2 WGDs in the vertebrate stem lineage followed by another WGD in early fish (e.g. [START_REF] Hoffmann | Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates[END_REF]; these WGDs are generally viewed to have provided the genetic diversity for many innovative vertebrate or fish specific characteristics and fueled their burst-like evolution. Recent polyploids are unusual, but have been found in individual species or lineages, for example, fish, amphibians, crabs or insects [START_REF] Mable | Genome duplication in amphibians and fish: an extended synthesis[END_REF][START_REF] Kenny | Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs[END_REF]. Differences between plant and animal reproduction have been proposed for the differential polyploid formation rate [START_REF] Coyne | Speciation[END_REF][START_REF] Husband | The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes[END_REF][START_REF] Otto | Polyploid incidence and evolution[END_REF]. Few animals, with the exception of protozoa and a few insect species, have the possibility of apomictic or the equivalent of vegetative reproduction. Even with mechanisms to ensure correct pairing of chromosomes in a polyploid (e.g. [START_REF] Sepsi | CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat[END_REF], the widespread occurrence of sex chromosomes in animals may also limit fertility in polyploid animals [START_REF] Collares-Pereira | Natural pathways towards polyploidy in animals: the Squalius alburnoides fish complex as a model system to study genome size and genome reorganization in polyploids[END_REF]. An evolutionary association between reproductive modes and polyploidy has been studied for decades (e.g. [START_REF] Stebbins | Variation and evolution in plants[END_REF] through two main aspects: the occurrence and rate of asexual vs. sexual reproduction on one side, and the transitions in mating systems (i.e. self-compatibility or sexual dimorphism) on the other side. When correlations have been detected, it has usually proven difficult to disentangle the causes and consequences of the different processes. As [START_REF] Ashman | Revisiting the dioecy-polyploidy association: alternate pathways and research opportunities[END_REF] showed, the observed association between sex dimorphism (e.g. dioecy) and polyploidy can be explained by direct or indirect effects of one process on the other, since evolutionary transitions usually occur simultaneously, and different factors can affect these transitions in different clades [START_REF] Glick | Polyploidy and sexual system in angiosperms: Is there an association?[END_REF]. The same questions hold for the association between self-fertilization and ploidy, since polyploidy usually correlates with self-compatibility [START_REF] Barringer | Polyploidy and self-fertilization in flowering plants[END_REF][START_REF] Husband | Mating consequences of polyploid evolution in flowering plants: current trends and insights from synthetic polyploids[END_REF][START_REF] Robertson | Comparative evidence for the correlated evolution of polyploidy and self-compatibility in Solanaceae[END_REF][START_REF] Alix | The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation[END_REF] even if exceptions have been reported (e.g. in the Fragaria genus; [START_REF] Liston | Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights[END_REF]. Thus, the evolutionary link between mating system and ploidy has been fairly well documented, but the association of polyploidy with asexual reproduction (beyond the odd-ploidies such as 3x or 5x), and particularly clonal reproduction (i.e. vegetative growth in plants), has been less studied, particularly in wild species. Three articles of this special issue deal with this question. [START_REF] Herben | Polyploid species rely on vegetative reproduction more than diploids: a re-examination of the old hypothesis[END_REF] report association of vegetative reproduction with polyploidy in a large, phylogenetically broad, sample of 900 European angiosperm species to infer macroevolutionary patterns of both traits, and examine their temporal trends. As hypothesized, they detect a signal of correlated evolution between polyploidy and vegetative growth, mostly mediated by increased distance of spread. This is nicely confirmed by experimental 'garden' data, which show that diploids rely more on seed reproduction whereas polyploids rely more on vegetative spread. They also show that vegetative reproduction may often evolve before polyploidisation and could then enhance the rates of polyploid speciation.

The evolutionary association between asexual production of seeds (i.e. apomixis) and polyploidy has been studied frequently, not least because gametophytic apomixis and polyploidisation share the same characteristic feature, the production of unreduced gametes [START_REF] Ramsey | Pathways, mechanisms, and rates of polyploid formation in flowering plants[END_REF][START_REF] Whitton | The dynamic nature of apomixis in the angiosperms[END_REF][START_REF] Husband | The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes[END_REF][START_REF] Majeský | The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts[END_REF]. Here, two papers study the dynamics of apomixis in a context of hybridisation and polyploidy. In the first paper, [START_REF] Uhrinová | Origin and genetic differentiation of pink-flowered Sorbus hybrids in the Western Carpathians[END_REF] assess the genetic relationships between parental and hybrid species in the genus Sorbus, which is known for exhibiting apomictic microspecies produced by hybridisation [START_REF] Robertson | Hybridization and polyploidy as drivers of continuing evolution and speciation in Sorbus[END_REF]. Three parental species, one a tetraploid species (S. chamaemespilus) and two mainly diploid cytotypes (S. aria and S. aucuparia), seem to have produced a set of genetically distinct polyploid microspecies through interspecific hybridisation. These polyploid species seem at least partially reproductively isolated and exhibit a low population genetic diversity compared to the parental species populations as well as a high rate of clonality. If this low diversity results from predominant apomixis, this would be another confirmation of the evolutionary link between apomixis and polyploid speciation through hybridisation, at least in the genus Sorbus. Similarly, ancient polyploid apomicts of the subgenus Rubus studied by Šarhanová et al. (2017) seem to have been maintained in central Europe without relying on their facultative sexuality but rather on hybridisation with a sexual species (mainly ser. Glandulosi). This process may regularly produce successful apomictic polyploid lineages but with low genetic polymorphism.

Polyploidy and ecological divergence

Over long evolutionary times, at least among angiosperms, new polyploid species have driven their diploid ancestors to extinction at several points (Fig. 1). However, open questions remain: Are most polyploid lineages evolutionary dead ends? Have particular events, such as changing climate, enabled polyploids to out-compete their diploid ancestors? Are any evolutionary recent (perhaps the last 5 million years) polyploids more successful than the equivalent diploids? Several authors have considered related questions about plant genome evolution [START_REF] Mayrose | Recently formed polyploid plants diversify at lower rates[END_REF][START_REF] Arrigo | Rarely successful polyploids and their legacy in plant genomes[END_REF][START_REF] Soltis | Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al[END_REF][START_REF] Vanneste | Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary[END_REF][START_REF] Mayrose | Methods for studying polyploidy diversification and the dead end hypothesis: a reply to Soltis et al[END_REF], some reflecting the biogeographical patterns of polyploid species and their relationship to ecological adaptation [START_REF] Madlung | Polyploidy and its effect on evolutionary success: old questions revisited with new tools[END_REF]e.g. Herklotz and Ritz, 2017).

It has been postulated for a long time that polyploidisation might be associated with particular and large species ranges and/or extreme habitats [START_REF] Stebbins | Variation and evolution in plants[END_REF][START_REF] Otto | Polyploid incidence and evolution[END_REF][START_REF] Levin | The role of chromosomal change in plant evolution[END_REF][START_REF] Husband | The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes[END_REF][START_REF] Weiss-Schneeweiss | Evolutionary consequences, constraints and potential of polyploidy in plants[END_REF]. Potentially contrasting results have been obtained from biogeographical surveys of polyploid and diploid species (e.g. [START_REF] Martin | Influence of phylogeny and ploidy on species ranges of North American angiosperms[END_REF][START_REF] Pandit | Ploidy influences rarity and invasiveness in plants[END_REF]. However, even environmental correlations (e.g. polyploidy associated with higher latitudes or particular climatic niches) do not necessarily imply ecological adaptation as an explanatory factor, since other processes such as demography (i.e. dispersal variance and genetic drift) can produce the same patterns.

Experimental designs such as reciprocal transplants can provide compelling evidence of adaptation of polyploids (e.g. [START_REF] Ramsey | Polyploidy and ecological adaptation in wild yarrow[END_REF][START_REF] Herben | Polyploid species rely on vegetative reproduction more than diploids: a re-examination of the old hypothesis[END_REF], although local biogeographical studies of sister or closely-related species can provide useful insights into the patterns of ecological divergence of polyploid and diploid species (e.g. [START_REF] Laport | Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex[END_REF]. In this volume, [START_REF] Paule | Ecological range shift in the polyploid members of the South American genus Fosterella (Bromeliaceae)[END_REF] assess the degree of ecological divergence of polyploid species from the bromeliad Fosterella in Andean mountains, in relation to historical biogeographical processes. Polyploids seem to occupy slightly divergent climatic niches but patterns of cytotype geographical distribution suggest a historical parapatric differentiation of polyploid species that has not necessarily been caused by ecological adaptation. Both processes are potentially at the origin of polyploid range shifts in this southern American species complex. This is also probably the case for the Mediterranean grass Anthoxanthum studied by [START_REF] Chumová | The Mediterranean: the cradle of Anthoxanthum (Poaceae) diploid diversity[END_REF].

They show that several diversification events might have taken place since the Miocene from a diploid ancestor, by recurrent range expansions possibly linked to climatic niche differentiation. THE GENOMIC CONFLICTS AWAKEN: POLYPLOIDY AS A PEACEKEEPER?

Apart from the presence of ancient or recent polyploidy, and the wide variation in chromosome number, the large variation in size of plant genomes is an enigma. Measured as the 1C or unreplicated haploid genome size, the range known is from 63 Mb for Genlisea margaretae to 149,000 Mb for Paris japonica [START_REF] Bennett | Nuclear DNA amounts in angiosperms: targets, trends and tomorrow[END_REF]. The "C-value paradox" after work of [START_REF] Swift | The constancy of desoxyribose nucleic acid in plant nuclei[END_REF] notes that there are few correlations between apparent organism characteristics and genome size (e.g. [START_REF] Freeling | A solution to the C-value paradox and the function of junk DNA: the genome balance hypothesis[END_REF]. For example, [START_REF] Krahulcová | Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)[END_REF] show no significant correlation between DNA content and seed size in nine Aesculus species. However, a correlation between plant genome size and content of transposable elements (TEs) has been observed [START_REF] Ågren | Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?[END_REF][START_REF] Negi | Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response[END_REF][START_REF] Pearce | The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation[END_REF], with LTR-retrotransposons being the most abundant source of genome size variation in many lineages [START_REF] Bennetzen | The contributions of transposable elements to the structure, function, and evolution of plant genomes[END_REF][START_REF] Biscotti | Repetitive DNA in eukaryotic genomes[END_REF]. In addition to polyploidy, TE activity (proliferation and/or elimination; [START_REF] Vitte | LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model[END_REF] is associated with genomic recombination and contributes to shape plant genomes by copy number increase (e.g. [START_REF] Santos | Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploidy Brachiaria forage grasses[END_REF], gene disruption (e.g. [START_REF] Tam | The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species[END_REF] or co-mobilizing of other sequences such as those associated with reproductive incompatibility [START_REF] Alix | The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation[END_REF].

Here, [START_REF] Vicient | Impact of transposable elements on polyploid plant genomes[END_REF] review the major contribution of TEs to plant genome diversity and evolution as well as to gene expression variation, focusing mainly on LTR-retrotransposons. In relation to their capacity to move across the genome and their close association with unequal and illegitimate recombination, TEs (notably LTR-retrotransposons) may generate a large variety of structural mutations that can be beneficial -even if they are more commonly detrimental or at least neutral. Such positive mutational TE insertions have represented interesting genomic targets for selection during plant domestication and crop breeding (for reviews [START_REF] Lisch | How important are transposons for plant evolution?[END_REF][START_REF] Vitte | The bright side of transposons in crop evolution[END_REF]. Transposable elements are usually targeted efficiently by epigenetic marks (including DNA methylation and post-translational modifications of histones) for ensuring their tight control to avoid any anarchical activation and transposition across the genome [START_REF] Mirouze | Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes[END_REF]. Stress conditions are assumed to reactivate TEs because of the extensive epigenetic remodeling of the genome they might trigger; interspecific hybridisation and polyploidy can act as such stresses (an implication of [START_REF] Mcclintock | The significance of responses of the genome to challenge[END_REF]reviewed by Parisod et al., 2010a). [START_REF] Vicient | Impact of transposable elements on polyploid plant genomes[END_REF] thus emphasize the close relationships between polyploidy and TE activity and the involvement of TEs in gene regulation in response to the epigenetic modifications associated to polyploidisation. The authors highlight the impact of mediated DNA methylation changes at TE insertion sites on the functional regulation of neighbouring genes, as found, for instance, in Arabidopsis in response to biotic stress [START_REF] Dowen | Widespread dynamic DNA methylation in response to biotic stress[END_REF] and in rice following polyploidisation [START_REF] Zhang | Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression[END_REF].

The major TE silencing mechanism in plants is the biogenesis of small non coding RNAs, known as small (or short) interfering RNAs (siRNAs), with populations of 21nucleotide-long (21-nt) siRNAs and mainly 24-nt siRNAs that control TEs by TGS (i.e. transcriptional gene silencing) through RNA-directed DNA methylation, RdDM [START_REF] Lewsey | Mobile small RNAs regulate genome-wide DNA methylation[END_REF]. Only a few studies have dealt with the immediate impact of polyploidy on the biogenesis of small RNA populations [START_REF] Ha | Small RNAs serve as genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids[END_REF][START_REF] Kenan-Eichler | Wheat hybridization and polyploidization results in deregulation of small RNAs[END_REF][START_REF] Palacios | Response of non-coding components of the genome -transposable elements and small non-coding RNAs -to a new allopolyploidisation event: the genome of oilseed rape (Brassica napus) as a model of study[END_REF][START_REF] Zhang | Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression[END_REF], but they all reported major changes in expression profiles of 24-nt siRNAs.

The responses of small RNAs to (allo)polyploidy, which also remind of the more general dynamics of small RNAs depicted in response to hybridisation, have progressively led to the idea of a major role of TE-derived siRNAs in the process of hybrid incompatibility (reviewed by [START_REF] Ng | Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility[END_REF]. At the onset of the hybrid or the neoallopolyploid formation is the necessity to overcome hybrid failure, which ranges from early seed inviability to hybrid sterility. Similar to parental imprinting in animals, genome reprogramming occurs in plants, but specifically in vegetative cells, with the loss of DNA methylation at the origin of transposable element reactivation, resulting in the production of novel TE-derived siRNAs [START_REF] Slotkin | Epigenetic reprogramming and small RNA silencing of transposable elements in pollen[END_REF]. If parental TE sequences differ substantially, often the case during interspecific hybridisation, TEderived siRNAs inherited from each parent represent key factors to control the reactivated TEs, and their efficiency in repressing TEs may determine the outcome of the interspecific cross [START_REF] Martienssen | Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis[END_REF].

Reproductive isolation, and particularly post-zygotic isolation, between plant and animal species is thought to often result from genomic conflicts involving selfish genetic elements [START_REF] Presgraves | The molecular evolutionary basis of species formation[END_REF][START_REF] Rieseberg | Speciation genes in plants[END_REF][START_REF] Ågren | Selfish genes and plant speciation[END_REF]. The view of polyploidy, and especially allopolyploidy, as a "peacekeeper" in genomic conflicts when two divergent genomes are brought together in hybrids is not new [START_REF] Rieseberg | Polyploid evolution: keeping the peace at genomic reunions[END_REF][START_REF] Tayalé | Natural pathways to polyploidy in plants and consequences for genome reorganization[END_REF], but it can also be viewed as generating conflicts that will have to be resolved in a more complex way [START_REF] Comai | The advantages and disadvantages of being polyploid[END_REF][START_REF] Jones | Genome conflict in the gramineae[END_REF]. These genomic conflicts can have multiple origins such as TE-mediated silencing misregulation or segregation distorters -e.g. female meiotic centromere drive or supernumerary chromosome drive [START_REF] Jones | Genome conflict in the gramineae[END_REF], and there are different ways by which allopolyploidisation can buffer their effects. First, when they are at the origin of epistatic autosomal Bateson-Dobzhansky-Muller (BDM) hybrid incompatibilities, they will be on average recessive and expressed mainly in F2 and subsequent generations. A direct consequence of polyploidisation will be to avoid expression of this kind of hybrid defect because recessive BDM factors will almost never be homozygous, provided that the recombination rate between homoeologous chromosomes is low. A related effect of this lack of recombination will be the proper segregation of chromosomes in allopolyploids compared to homoploid hybrids [START_REF] Tayalé | Natural pathways to polyploidy in plants and consequences for genome reorganization[END_REF].

Second, hybrid incompatibilities due to divergent gene expression (e.g. for parentally imprinted genes) or subfunctionalisation of duplicate genes will have potentially no effect in polyploids.

Third, polyploidisation could facilitate the occurrence of apomixis by involving low recombination, heterochromatic regions behaving as selfish genetic elements, such as supernumerary chromosomes [START_REF] Roche | Is supernumerary chromatin involved in gametophytic apomixis of polyploid plants?[END_REF][START_REF] Comai | The advantages and disadvantages of being polyploid[END_REF], and providing in turn an advantage for propagating the new species in the first generations. Finally, diploid hybrid defects as well as dosage-related problems specific to polyploidisation will be overcome, usually in later generations, by gene expression remodelling and/or chromosomal rearrangements and gene loss [START_REF] Chen | Genetic and epigenetic mechanisms for polyploidy and hybridity[END_REF]. The modulation of gene regulation, including genome dominance in polyploids [START_REF] Woodhouse | Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids[END_REF], is probably important for the success or evolutionary failure of a new hybrid.

The epigenetic control of genomic conflicts determining the viability of hybrids opens new avenues of investigation, which include that of the evolutionary significance of epigenetic regulation in the success of interspecific hybridisation and allopolyploidy and the differential control of multiple genomes.

CONCLUSION AND PERSPECTIVES

Polyploidy is arguably the major feature of plant genome evolution, doubling the number of copies of each gene with each whole genome duplication event. Over evolutionary time, polyploids have displaced all their diploid ancestors several times in multiple independent lineages, suggesting a strong selective advantage. These multiple polyploid events have only been detected thanks to widespread large-scale whole genome sequencing since 2000, and comparative genomic analyses continue to reveal the recurrence and extent of WGD along the evolutionary history of plant lineages (Fig. 1). The "-omics" era has allowed understanding of the evolutionary history of lineages (e.g. [START_REF] Douglas | Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris[END_REF][START_REF] Roux | Inferring the mode of origin of polyploid species from nextgeneration sequence data[END_REF][START_REF] Wendel | The wondrous cycles of polyploidy in plants[END_REF][START_REF] Woodhouse | Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids[END_REF][START_REF] Barker | Spreading wine and flying high: the evolutionary importance of polyploidy after a century of study[END_REF]. Several of the most important angiosperm groups include a WGD event that is detected soon after the Cretaceous-Tertiary (KT) extinction event (Fig. 1); one can speculate that their genetic structure enabled these polyploids to thrive.

One can ask if new polyploids may once again have advantages during the global events including widespread extinction (see [START_REF] Parmesan | Plants and climate change: complexities and surprises[END_REF] now being detected, including climate change. Plants have genetic mechanisms to overcome the challenges of polyploidy, in particular co-regulation of multiple, similar or identical copies of genes, and the adoption of vegetative or apomictic reproduction, or restitution of diploid behaviour during chromosome pairing and recombination at meiosis. Now, we can identify the impact of polyploidy, and associated hybridity, on speciation, regulatory mechanisms at the gene expression level, and examine its impact on plant populations, as reported in this Special Issue.

suggested the range of 167-199 million years ago (Mya) [START_REF] Bell | The age and diversification of the angiosperms rerevisited[END_REF]. Then rapid radiations responsible for the extant angiosperm diversity occurred after the early diversification of Mesangiospermae 139-156 Mya [START_REF] Moore | Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms[END_REF][START_REF] Bell | The age and diversification of the angiosperms rerevisited[END_REF] with a burst of diversification specific of the Cretaceous, less than 125 Mya (age of the earliest angiosperm macrofossil; [START_REF] Cascales-Miñana | Is Darwin's 'Abominable Mystery' still a mystery today?[END_REF].

Early divergence times are from [START_REF] Bell | The age and diversification of the angiosperms rerevisited[END_REF] and [START_REF] Leliaert | Phylogeny and Molecular Evolution of the Green Algae[END_REF]; for angiosperms from [START_REF] Fawcett | Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event[END_REF], [START_REF] Jiao | Ancestral polyploidy in seed plants and angiosperms[END_REF] and [START_REF] Li | Gene duplicability of core genes is highly consistent across all angiosperms[END_REF] and for gymnosperms from [START_REF] Lu | Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes[END_REF]. Dashed lines indicate imprecise timing or approximate representation of lineage divergence. WGD events are from [START_REF] Jiao | Ancestral polyploidy in seed plants and angiosperms[END_REF]Leliart et al. (2011);[START_REF] Hont | The banana (Musa acuminata) genome and the evolution of monocotyledonous plants[END_REF]; [START_REF] Beike | Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex[END_REF]; Renny-Byfield and Wendel (2014); [START_REF] Li | Early genome duplications in conifers and other seed plants[END_REF][START_REF] Apg Iv | An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV[END_REF]; [START_REF] Scott | Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers[END_REF]; [START_REF] Shaw | Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)[END_REF] [START_REF] Bombarely | Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida[END_REF]. See corresponding publications for precise estimates of time divergence and occurrence of WGD. AGF: hypothetical ancestral green flagellate; ANA: basal angiosperms including Amborellales, Nymphaeales, Austrobaileyales; following a standardized method, Greek letters are used to name polyploidy events along the phylogenetic tree, starting from the α (alpha) and β (beta) events that have been identified in the Arabidopsis genome [START_REF] Bowers | Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events[END_REF]. Cretaceous-Tertiary extinction event Vitis (grapevine) Solanum (tomato, potato) Arabidopsis Carica (papaya) Populus (poplar) Linum (flax) Brassica (kale, rapeseed) Glycine (soybean) Malus (apple tree) Musa (banana) Oryza (rice) Triticum (wheat) Zea (maize)

Figure 2 .

 2 Figure 2. Metaphase chromosomes of diploid, tetraploid and hexaploid wheats stained

  . 2017. Annals of Botany. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants.

  Figure 2

ACKNOWLEDGEMENTS

We particularly thank Eric Jenczewski for helpful discussions, and Alessandra Contento for the images shown in Figure 2. We also thank Zuzana Münzbergová and two anonymous referees for their helpful comments on our manuscript. We finally thank all our colleagues and collaborators, as well as our students and postdocs for their contribution to our work on polyploidy and interspecific hybridisation in plant genome evolution.


David Berthebaud

Fabien Grasset
email: grasset@univ-rennes1.fr.

Vincent Allegret-Maret

Soraya Ababou-Girard

Stanislav Pechev

Tunable optical absorption on "ZnxTixO4-3yN2y" nanosized spinel powders

come

Introduction

Nanomaterials represent a new class of materials with continuously increasing fields of applicationsenvironment, catalysis, biotechnology, and magnetic and optical devices. Particularly, nanoparticles have generated a large research effort in the past 10 years because their properties differ markedly from those of their bulk counterpart. [START_REF] Klabunde | Nanoscale Materials in Chemistry[END_REF] Recently, we developed a new low-cost colloidal sol-gel route to prepare nanosized colored "ZnTiON", 1 µm thick, porous layers on glass. [START_REF] Grasset | [END_REF] First, we had prepared highly concentrated ZnO nanocolloids using an alcoholic clusters route developed in refs 3 and 4. Then we added titanium tetraisopropoxide in order to obtain new Ti 4+ @ZnO nanocolloids. To get colored oxynitrides, we used an ammonia-induced replacement of oxygen by nitrogen according to the general equation oxide + NH 3 f oxynitrides + H 2 O, well-known from classical solid-state chemistry. 5 These kinds of colored porous thin films showed excellent photostability and photodegradation of an aqueous methylene blue solution in the visible spectrum. [START_REF] Grasset | [END_REF][START_REF] Spanhel | Proceedings of 17th Workshop on Quantum Solar Energy ConVersion (QUANTSOL 2005)[END_REF] These results corroborate recent works about oxynitrides or nitrogen-doped oxides reporting high photocatalytic activity under visible light (refs 7 and 8 and references therein). In this paper, we present the microstructural characterization of "ZnTiON" nanosized powders obtained from nanocolloids. The nanosized powders were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoemission spectroscopy (XPS), oxygen and nitrogen analysis, and UV-vis spectroscopy.

Experimental Section

Synthesis Process. The nanosized powders were synthesized from Ti 4+ @ZnO nanocolloids by evaporation of alcohol using a rotating evaporator. Briefly, Ti 4+ @ZnO nanocolloids were prepared using zinc acetate dihydrate (4.39 g) suspended in n-propanol (40 mL) under ambient atmosphere and distilled for 10 min in a preheated silicon oil bath (125 °C). Under magnetic stirring, methanolic tetramethylammonium hydroxide (TMAH) base solution was rapidly added (9 mL, 2.37 M) to the still hot precursor (45 °C), yielding initially a turbid precipitate which next turned into a clear nanocolloid after a few minutes. To the fresh sol, we added titanium tetraisopropoxide precursor (Zn/ Ti ) 1), which readily reacts with the ZnO nanocrystals. After cooling to room temperature, the solvant was removed using a rotary evaporator (40 °C, 20 Pa). The resulting soft-gel was then kept in an oven at 100 °C during 1 week in order to solidify, then was ground and pre-sintered at 400 °C in air to remove the organic residues, and finally transformed into white powder. To get colored oxynitrides, the powders (0.5 g) are annealed under ammonia gas (purity N36) for 1 h at temperatures between 550 and 750 °C and then cooled by removing the electrical power under ammonia flow.

Elemental Analysis. Nitrogen and oxygen contents were determined with a TC-436 analyzer from LECO, Inc. using the inert gas fusion method, nitrogen as N 2 by thermal conductivity, and oxygen as CO 2 by infrared detection. The apparatus was calibrated with N 2 and CO 2 gas (purity, 99.95%). At least three analyses were performed for each sample in the same conditions.

X-ray Intensity Measurements and Peak Profile Analysis. The powder X-ray diffraction data were recorded at diffractometers with Bragg-Brentano geometry, Cu KR radiation (40 kV, 30 ÷ 40 mA, and 0.5 ÷ 10 s integration time), proportional detectors, and secondary monochromators. At room temperature a Philips PW 3020 was used. The high-temperature XRD experiments were performed on a Philips X'Pert MPD with an Anton Paar HTK-16 camera, where the powder sample is deposed directly on the heating elementsa platinum strip.

The average apparent crystallite size ( β ) was evaluated from a whole diffraction pattern profile analysis, using last developments implemented in the Fullprof program (version 2.0 Nov 2001, LLB, Juan Rodriguez-Carvajal). A normalized Voigt function (convolution of Gaussian and Lorentzian functions) was used to fit the peak profiles. The profile analysis is based on the angular dependence of the full width at half-maximum (FWHM) of the Gaussian and Lorentzian components (H G and H L , respectively). Both instrumental and sample intrinsic contributions to the line broadening were examined separately. When the instrumental resolution function (IRF) is known, the sample contribution to the line profile is calculated as follows:

where U strain iso , X strain iso , G size iso , and Y size iso are refinable parameters related to isotropic size and strain effects on the line broadening, while D strain aniso and F size aniso are analytical functions for an hkl-dependent broadening model. ξ is a mixing coefficient for the Lorentzian part of the strains. The integral-breadth method is applied, finally, to determine the crystallite size and strains in the sample. "Perfect" Y 2 O 3 powder was used as a standard to determine the resolution function of the diffractometer. The observed line broadening was modeled by considering isotropic size and strain contributions. Only the size-related terms of H G and H L (G size iso and Y size iso ) converged to significant values. The strain-dependent parameters (U strain iso and X strain iso ) had meaningless values, which did not influence the profile fitting of the XRD patterns. After the profile refinement, the apparent size along each reciprocal lattice vector is calculated. The average apparent crystallite size ( β ) can be related to the true size, but only if the crystallite shape is known or assumed. For instance, for a spherical crystallite, the true diameter D is simply given by 4/3( β ). Moreover, this simple relation is strictly valid for a monodisperse system. 9 So, the true size could be defined only in the case of single-domain nanoparticles without amorphous shell, as it is for transmission electron microscopy (TEM) and/or scanning electron microscopy (SEM) images.

Morphological Investigations by SEM. SEM photographs were taken by JEOL JSM 6301F microscope to examine the shape and size of the nanoparticles.

UV-Vis Spectroscopy. Diffuse reflectance spectra were collected using a UV-vis CARY 100 spectrometer equipped with a Labsphere DRA-CA-30I with a 70 mm diameter coated with Spectralon (PTFE). The absolute reflectance of the sample is compared with a calibrated 2 in. D 99% Spectralon reflectance standard.

X-ray Photoemission Spectroscopy. XPS was performed under a base pressure of 5 × 10 -9 mbar using a VSW HA100 spectrometer. The analyzer was operated with at constant pass energy of 22 eV, which leads to an experimental resolution of 1.1 eV. The X-ray source used either Al or Mg KR excitation radiation at 1486.6 and 1283.6 eV, respectively. The spectrometer binding energy scale was initially calibrated against the Au 4f7/2 (84.0 eV) level and Cu 2p3/2 (932.7 eV). Since the films were nonconductive, they were referenced to adventitious hydrocarbon with C1s binding energy at 284.9 eV

Results and Discussion

Using the described soft method to synthesize ZnO nanocolloids, the hydrodynamic diameter of the ZnO nanoparticles is around 7 nm. 10 Nevertheless, analysis of the X-ray powder

H G 2 ) (U strain iso + (1 -ξ) 2 D strain aniso 2 )tg 2 θ + G size iso cos 2 θ
H L ) (X strain iso + ξD strain aniso )tgθ + Y size iso + F size aniso cos θ diffraction data of the Ti@ZnO solid gel obtained after removing the alcohol show amorphous structure (Figure 1). This amorphous structure can be explain by the fact that Ti 4+ tetraisopropoxide (i) partly decomposes the ZnO nanocrystals (this has been confirmed by XRD in this work and in complementary UV-vis absorption and DLS measurements in our previous work 10 ); (ii) forms itself into amorphous compounds at room temperature. In fact, XRD data reveal that the decomposition of ZnO nanoparticles is dependent on the amount of titanium tetraisopropoxide added into the ZnO nanocolloids. In Figure 1, the X-ray patterns of two different Zn/Ti ratios are represented. We notice that the peaks of ZnO appear with the ratio Zn/Ti ) 2, whereas they are not present for the Zn/Ti ) 1 ratio.

In situ temperature-dependent X-ray diffraction in air shows that above 150 °C, for the Zn/Ti ) 1 ratio, peaks of zinc oxide appear again (Figure 2). The binary compounds in the system Zn-Ti-O can be detected only at 500 °C, and no pure phase could be prepared in air until 600 °C. The presence of ZnTiO 3 (JCPDS card n°26-1500) and Zn 2 Ti 3 O 8 phases as impurity agrees with the Zn-Ti-O phase diagram. 11 X-ray diffraction under ammonia atmosphere with our laboratory apparatus was not possible because of the high activity of ammonia gas. Only pure phases were prepared from annealed solid-gel (i) at 400 °C in air and (ii) using ammonia atmosphere with a temperature higher than 550 °C (Figure 3). Analysis of the room-temperature X-ray powder diffraction data indicates that "ZnTiON" compounds annealed between 600 and 750 °C are isostructural with a cations deficient spinel type structure such as Zn 2 Τi 3 O 8 (a ) 8.390 Å). 13 The observed XRD patterns were refined using the Le Bail method. The refined values of the lattice parameters and the average apparent crystallite size ( b ), extracted from the line profile fit are given in Table 1.

The observed, calculated, and difference X-ray diffraction profiles for the compound annealed at 750 °C are shown as examples in Figure 4. Classically, Fd3 hm is used as the space group for spinel type structure, but the defect spinel that exhibits ordered cation vacancies should be indexed with P4 1 32. 12,13 This ordering leads to a space group with lower symmetry. The evaluated β were estimated within a range between 4.2 and 15.4 nm, which is in good agreement with the powder SEM images (Figure 5).

As expected, the β is increasing with the annealing temperature. These results agree with high-resolution transmission electron microscopy (HRTEM) and XRD data on thin film reported in ref 2. In fact, our previously obtained HRTEM images of the films have shown a broad scale of differently sized nanodomains ranging between 1 and 9 nm, the β increasing also with the annealing temperature. This point has been confirmed by the SEM images (Figure 5) of the powder.

Above the dissociation temperature of ammonia, the optical transmission spectra are progressively red-shifted with increasing nitriding temperature. As observed in Figure 6, the progressive N 3-/O 2-anionic substitution gives the possibility to tune the absorption edge position by varying the nitridation temperature. This red shift is directly related to the nitrogen content determined by LECO apparatus (Table 1) and coincides with the observation generally made for micrometer-sized nitrided oxide powders. 14 In our previous papers, 2,10 the presence of N 3-was confirmed on colored thin film by XPS techniques (the N K-edge located at 396.1 eV proves the presence of oxynitrides). In addition, when raising the nitridation temperature, a new Ti(2) component appears at the low-energy side of the XPS-Ti spectra which is related to the nitrogen incorporation. This new component was attributed to Ti-N bounds. [START_REF] Grasset | [END_REF]10 In the present case of nanosized powders, preliminary XPS analysis of Zn and Ti reveals that after 1 h treatment under ammonia at 600 and 650 °C the Zn/ Ti remains close to 1. Using all these results, a chemical formula could be proposed for the compounds annealed at 600 and 650 °C (Table 1), keeping the Zn/Ti ratio equal to 1. As an example, the chemical formula for the compound annealed at 650 °C could be written as Zn 1.33 Ti 1.33 0 0.33 O 3.49 N 0.34 0 0.17 following ref 15. For higher temperature, analysis is in progress. Nevertheless we could expect some nonstable phases because LECO analyses show that, for temperatures higher than 800 °C, the nitrogen content decreases. The powder slightly becomes green-yellow, indicating a metal reduction process. 16 This phenomenon has been already observed for micrometer-sized powder oxynitridess the nitrogen content reaches a maximum when the temperature is increased and then it decreases due to the volatilization or the reduction of metal. 15 As a result, the domain of existence of "ZnTiON" oxynitrides is limited in temperature (between 550 and 800 °C). Moreover, thermogravimetric measurement (temperature rate, 10 °C/min) shows that these oxynitrides are stable in air until 430 °C; a further increase of the weight indicates an oxidation process. Nevertheless, we notice that, thanks to our nanocolloid approach, pure oxynitride phases were obtained only after 1 h (only 15 min for 1 µm thick film) of annealing time under ammonia flow, whereas the classical nitridation process usually takes several hours. 15

Conclusion

We are able to prepare new spinel oxynitride compounds with tunable band gap from white to yellow colors. A chemical formula is proposed for the compounds annealed at 600 or 650 °C, and it could be written as "Zn 1.33 Ti 1.33 O 4-3y N 2y ". These compounds present promising semiconducting properties for potential gas sensing or sunscreen applications. BATCH: jp6b254 USER: jwm29 DIV: @xyv04/data1/CLS_pj/GRP_jy/JOB_i23/DIV_jp0716334 DATE: May 10, 2007

Figure 1 .

 1 Figure 1. X-ray diffraction at 25 °C of nanopowders with Zn/Ti ) 1 (a) and Zn/Ti ) 2 (b) ratios. (Pt ) platinum sample holder; / ) ZnO main peaks.)

  BATCH: jp6b254 USER: jwm29 DIV: @xyv04/data1/CLS_pj/GRP_jy/JOB_i23/DIV_jp0716334 DATE: May 10, 2007 B J. Phys. Chem. C Grasset et al.

Figure 2 .

 2 Figure 2. Temperature-dependent X-ray diffraction under air atmosphere.

Figure 3 .

 3 Figure 3. XRD patterns of "ZnTiON" oxynitrides powder.

Figure 4 .

 4 Figure 4. Observed, calculated, and difference X-ray diffraction profiles for the compound annealed at 750 °C.

Figure 5 .

 5 Figure 5. SEM images of nanosized powder annealed at 400 °C under air (a) and 700 °C under ammonia flow (b).

Figure 6 .

 6 Figure 6. Changes in the optical transmission spectra of "ZnTiON" nanosized powders with increasing nitriding temperature.

TABLE 1 : LECO Analysis and XRD Results

 1 Taking the density into account. 0 represents vacancy. BATCH: jp6b254 USER: jwm29 DIV: @xyv04/data1/CLS_pj/GRP_jy/JOB_i23/DIV_jp0716334 DATE: May 10, 2007 D J. Phys. Chem. C Grasset et al.

	temp (°C)	O (wt %)	N (wt %)	cell param (nm)	chem composn a	β (nm)
	600 (NH3)	27.7	1.8	8.430(1)	Zn1.33Ti1.3300.33O3.65N0.2400.11	4.2(5)
	650 (NH3)	25.9	2.5	8.430(1)	Zn1.33Ti1.3300.33O3.49N0.3400.17	7.3(5)
	700 (NH3)	24.9	3.0	8.441(1)		11.0(5)
	750 (NH3)	23.8	3.6	8.441(1)		14.3(5)
	800 (NH3)	25.8	2.5	8.438(1)		15.4(5)
	158
	159
	160
	161
	162
	163
	164
	165
	166
	167
	168
	169
	170
	171
	172
	173
	174
	175
	176
	177
	178
	179

a

Acknowledgment. The authors thank N. Pontais for providing LECO analysis, F. Tessier for X-ray measurements facilities, Prof. Marchand for helpful discussion, and M. J. Le Lannic for supplying the SEM images.


Ruslan Kalendar
email: ruslan.kalendar@helsinki.fi

Karine Alix

Francois Sabot

Fernando Rodriguez

Gennady I Karlov

Lucia Natali

Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools

Keywords: plant genome evolution, transposable elements (TE), retrotransposon (RTN), retrotransposon

Editorial on the Research Topic Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools

TRANSPOSABLE ELEMENTS TURN OUT TO BE FUNCTIONAL

Multiple changes that occur constantly in the plant genome allow an organism to develop from a single-celled embryo to a multicellular organism. A significant part of these changes is associated with the recombination activity of numerous classes of interspersed repeats. These numerous families of interspersed repeats were often called "junk DNA" as first, they were not associated with any vital protein-coding processes. Now, more and more clues indicate that such repeated DNA might play major roles in the genome as functional "non-coding" DNA [START_REF] Pennisi | Genomics. ENCODE project writes eulogy for junk DNA[END_REF][START_REF] Ariel | When junk DNA turns functional: transposon-derived non-coding RNAs in plants[END_REF]. Transposable elements (TEs), such as DNA transposons and retrotransposons, are the main part of these interspersed repeats [START_REF] Vitte | The bright side of transposons in crop evolution[END_REF]. The diverse families of retrotransposons are highly abundant genetic elements that are related to retroviruses [START_REF] Wicker | A unified classification system for eukaryotic transposable elements[END_REF]. Although retrotransposons are not "true" mobile elements like DNA transposons-from the comparison of their transposition mechanisms, retrotransposable elements (RTEs) are notably constitutive of heterochromatin and form a variety of major chromosomal structures such as centromeres [START_REF] Bennetzen | The contributions of transposable elements to the structure, function, and evolution of plant genomes[END_REF] and represent the main intergenic part of the plant genome [START_REF] Kalendar | Long tandem arrays of cassandra retroelements and their role in genome dynamics in plants[END_REF]. RTE mobility is ensured through an RNA intermediate, allowing a Copy-And-Paste approach for their transposition. Their own-encoded RNA is reverse transcribed using their own (or not) encoded enzymes, that will re-create from the single-strand RNA matrix a double-strand DNA at a new location. This reverse transcription can be either through extra-chromosomal DNA within a nucleocapsid (e.g., and implies RT/RNAseH + INT enzymes for LTR retrotransposons) or directly at the insertion site (e.g., Target-Prime Reverse transcription mechanism, with only the RT as a minimal set of enzymes for LINEs and SINEs; [START_REF] Wicker | A unified classification system for eukaryotic transposable elements[END_REF]. Such Copy-And-Paste mechanisms allow a quick invasion of naive genomes, and is responsible for massive genome increase in a few periods of time [START_REF] Piegu | Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice[END_REF]. Such invasions belong to a few number of initial active copies, called Master copies; however, while these copies must be transcriptionally active (i.e., able to produce RNA), they can be translationally inactive and may rely on other copies for enzymatic activities [START_REF] Sabot | Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome[END_REF]. When recently inserted, neo-copies can be related phylogenetically because of their sequence identity; subsequent mutations (point mutation, recombination, and so on) will then occur and their lineage can then be complex to recompose. Once inserted, each copy has its own evolutionary history and some may acquire biological role (or some part of the copy) and being excepted by their host. Some RTEs can provide evolutionary advantages to the host and were demonstrated to play a significant role in plant adaptation [START_REF] Song | Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice[END_REF]. If the fact that TEs can be beneficial to the host is now accepted, recent advances in the field has placed RTEs at the center of the current debate on eukaryotic and notably plant evolution. To advance this important research field, in the Research Topic "Mobile Elements and Plant Genome Evolution, Comparative Analyses, and Computational Tools" we focused on the efficiency of new genomic tools for the discovery of TEs, and some recent studies on the role of mobile elements in the evolution of the host genome, as well as on genome-wide comparative analysis and profiling of transposable elements.

MOBILE ELEMENT AND HOST GENOME EVOLUTION

Different retrotransposon families, each with its own lineage and structure, may have been active at distinct phases in the evolution of a species. Retrotransposon sequences bear the promoters that bind the nuclear factors of transcription initialization and initiate RNA synthesis by polymerases II or III. In the article entitled "Additional ORFs in Plant LTR-Retrotransposons" by Vicient and Casacuberta, LTR-retrotransposons that carry additional but not retrotransposon-specific open reading frames (aORF) were discovered and analyzed. This discovery reinforces the unique potential of LTR-retrotransposons as evolutionary tools, thanks to their ability to provide new genetic variants within a genome. The presence of antisense aORFs in characterized LTR-retrotransposon families from various angiosperm species indicates a putative role of these coding regions in the transposition process. To clarify the functions of these aORFs, further analysis of TE transcript splicing variants and thus access to the TE functional diversity would be very valuable.

TRANSPOSABLE ELEMENTS AS DRIVERS OF STRUCTURAL AND FUNCTIONAL VARIATIONS

Thanks to their remarkable diversity in size, genomic organization and transposition process, TEs are important drivers of genome evolution and species diversity [START_REF] Vicient | Impact of transposable elements on polyploid plant genomes[END_REF]. Keidar-Friedman et al. and Bariah et al. reported the potential impact of miniature transposable element insertions on the expression of genes in different wheat species, with the articles entitled "The Evolutionary Dynamics of a Novel Miniature Transposable Element in the Wheat Genome" and "Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome." TE-mediated genomic rearrangements and insertions of mobile genetic elements in gene-rich regions may act as mutagens and contribute to genome alteration [START_REF] Vicient | Impact of transposable elements on polyploid plant genomes[END_REF]. TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Potential TEs also contribute to genome plasticity and have a dramatic impact on the genetic diversity and evolution of the wheat genome. Using transposon display [START_REF] Kalendar | Palindromic sequence-targeted (PST) PCR, version 2: an advanced method for high-throughput targeted gene characterization and transposon display[END_REF] and genome-wide profiling analysis of insertional polymorphisms of transposable elements [START_REF] Kalendar | IRAP and REMAP for retrotransposonbased genotyping and fingerprinting[END_REF], the authors discovered large genomic rearrangement events, such as deletions and introgressions in the wheat genome. Highthroughput bioinformatics with next-generation sequencing (NGS) were key tools in these studies [START_REF] Vondrak | Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats[END_REF]. Structural rearrangements, gene duplications, and variation in TE contents may have a large impact on the overall genomic structure and may be responsible for phenotypic diversity [START_REF] Belyayev | Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat[END_REF]. In the article entitled "Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa, " Boutte et al. investigated structural variants and changes in the repetitive fraction between two accessions of Brassica rapa, and characterized genome-size variation among a core collection, using comparative genomics and cytogenetic approaches. Detection of large genomic variants between different cultigroups of the same species B. rapa highlighted the potential impact of the differential insertion dynamics of repeated elements in the intraspecific variability of genome size and chromosomal structure. This study also justifies the recent and general effort to construct pangenomes when access to the genomic diversity of a given species is sought.

TEs contribute also to the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic instability and evolution. Remnants of RTEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation. In the article entitled "Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding, " Pan et al. revealed that post-polyploidization of cotton genome instability resulted in numerous genomic structural changes that were accompanied by the expansion of LTR-retrotransposon families with an unbalanced contribution from the constituent genomes of cotton, with TEs from the D-genome being more active than TEs from the A-genome. This study also demonstrated that TE transposition activity coincided with cotton genome divergence, supporting the major role of TEs in genome shaping and speciation. Finally, the authors depicted the evolutionary past of cotton plants, which were recursively affected by polyploidization, like all plant lineages [START_REF] Alix | Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants[END_REF]: a decaploidization contributed to the formation of the genus Gossypium prior to the wellknown neo-tetraploidization that accompanied the formation of the currently widely cultivated cotton species. The resulting functional innovation comes directly from the diversity of duplicated genes, as suggested by their uncommonly high evolutionary rates.

CHROMOSOME EVOLUTION WITH TRANSPOSABLE ELEMENTS AND SATELLITE DNAS

The centromere is the unique part of the chromosome that combines a highly conserved function with a large variability of its constituent DNA sequences. In the article entitled "Functional Allium fistulosum centromeres comprise arrays of a long satellite repeat, insertions of retrotransposons and chloroplast DNA" Kirov et al. studied the functional centromere organization in the large-sized chromosomes of the species Allium fistulosum and A. cepa. They demonstrate that long and high-copy repeats are associated with insertions of retrotransposons and chloroplast DNA sequences, with tandem repeats being also constitutive of the centromeres. This article provides an insight into the major role of repetitive DNA in centromere function. Among evolutionary factors, repetitive sequences play multiple roles notably in sex chromosome evolution. As such, the Spinacia genus serves as an ideal model to investigate the evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. This was studied in the article entitled "Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Light on Their Roles in Sex Chromosome Evolution" by Li et al. Major repetitive sequence classes were identified in male and female genomes of Spinacia species and their ancestral relative sugar beet in order to decipher the evolutionary processes of sex chromosome evolution using NGS data. The differences of repetitive DNA sequences correlate with the formation of sex chromosomes and satellite DNAs are highly accumulated at the sex determination locus, demonstrating the role of repetitive DNA in sex chromosome evolution.

Frontiers in Plant Science | www.frontiersin.org

September 2021 | Volume 12 | Article 735134

ACKNOWLEDGMENTS

We thank all authors and reviewers for their contributions to this special issue and the support of the editorial office.

FUNDING

This work was supported by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan in the framework of program funding for research (AP08855353).

AUTHOR CONTRIBUTIONS

RK, FS, and KA prepared the draft. All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.

Conflict of Interest:

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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