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1. Combined cytogenetic and molecular methods for taxonomic verification and description of Brassica populations deriving from different origins

Author: Cyril Falentin, Houria Hadj-Arab, Fella Aissiou, Claudia Bartoli, Giuseppe Bazan, Matéo Boudet, Lydia Bousset-Vaslin, Marwa Chouikhi, Olivier Coriton, Gwénaelle Deniot, Julie Ferreira de Carvalho, Laurène Gay, Anna Geraci, Pascal Glory, Virginie Huteau, Riadh Ilahy, Vincenzo Ilardi, José A. Jarillo, Vladimir Meglic, Elisabetta Oddo, Monica Pernas, Manuel Pineiro, Barbara Pipan, Thouraya Rhim, Vincent Richer, Fulvia Rizza, Joelle Ronfort, Mathieu Rousseau-Gueutin, Rosario Schicchi, Lovro Sinkovic, Maryse Taburel, Valeria Terzi, Sylvain Théréné, Mathieu Tiret, Imen Tlili, Marie-Hélène Wagner, Franz Werner Badeck, and Anne-Marie Chèvre
Subjects: wild populations, landraces, Brassica, Genetic diversity, Genetics, QH426-470
Abstract: Agriculture faces great challenges to overcome global warming and improve system sustainability, requiring access to novel genetic diversity. So far, wild populations and local landraces remain poorly explored. This is notably the case for the two diploid species, Brassica oleracea L. (CC, 2n=2x=18) and B. rapa L. (AA, 2n=2x=20). In order to explore the genetic diversity in both species, we have collected populations in their centre of origin, the Mediterranean basin, on a large contrasting climatic and soil gradient from northern Europe to southern sub-Saharan regions. In these areas, we also collected 14 populations belonging to five B. oleracea closely related species. Our objective was to ensure the absence of species misidentification at the seedling stage among the populations collected and to describe thereafter their origins. We combined flow cytometry, sequencing of a species-specific chloroplast genomic region, as well as cytogenetic analyses in case of unexpected results for taxonomic verification. Out of the 112 B. oleracea and 154 B. rapa populations collected, 103 and 146, respectively, presented a good germination rate and eighteen populations were misidentified. The most frequent mistake was the confusion of these diploid species with B. napus. Additionally for B. rapa, two autotetraploid populations were observed. Habitats of the collected and confirmed wild populations and landraces are described in this study. The unique plant material described here will serve to investigate the genomic regions involved in adaptation to climate and microbiota within the framework of the H2020 Prima project ‘BrasExplor’.
Published: 2024
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2. Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)

Author: Delphine Giraud, Oscar Lima, Mathieu Rousseau-Gueutin, Armel Salmon, and Malika Aïnouche
Subjects: allopolyploidy, hybridization, transcriptome evolution, transposable elements (TE), Spartina, Genetics, QH426-470
Abstract: Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6–10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (
Published: 2021
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3. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Author: Julien Boutte, Loeiz Maillet, Thomas Chaussepied, Sébastien Letort, Jean-Marc Aury, Caroline Belser, Franz Boideau, Anael Brunet, Olivier Coriton, Gwenaëlle Deniot, Cyril Falentin, Virginie Huteau, Maryse Lodé-Taburel, Jérôme Morice, Gwenn Trotoux, Anne-Marie Chèvre, Mathieu Rousseau-Gueutin, and Julie Ferreira de Carvalho
Subjects: Brassica, genome evolution, transposable elements, LTR Gypsy, intraspecific diversity, ribosomal DNA, Plant culture, SB1-1110
Abstract: Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome vs. the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu.’ Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.
Published: 2020
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4. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency

Author: Franz Boideau, Alexandre Pelé, Coleen Tanguy, Gwenn Trotoux, Frédérique Eber, Loeiz Maillet, Marie Gilet, Maryse Lodé-Taburel, Virginie Huteau, Jérôme Morice, Olivier Coriton, Cyril Falentin, Régine Delourme, Mathieu Rousseau-Gueutin, and Anne-Marie Chèvre
Subjects: recombination rate and distribution, polyploidy, allotriploidy, Brassica napus, genetic mapping, plant breeding, Biology (General), QH301-705.5
Abstract: Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
Published: 2021
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5. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Author: Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chèvre, Patrick Wincker, Mathieu Rousseau-Gueutin, and Jean-Marc Aury
Subjects: genome, assembly, scaffolding, chromosome-scale, nanopore, optical map, Biology (General), QH301-705.5
Abstract: With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.
Published: 2021
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6. The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized Allotetraploid Brassica napus L.

Author: Mathieu Rousseau-Gueutin, Jérôme Morice, Olivier Coriton, Virginie Huteau, Gwenn Trotoux, Sylvie Nègre, Cyril Falentin, Gwennaëlle Deniot, Marie Gilet, Frédérique Eber, Alexandre Pelé, Sonia Vautrin, Joëlle Fourment, Maryse Lodé, Hélène Bergès, and Anne-Marie Chèvre
Subjects: Brassica napus, allopolyploidy, genome dynamic, meiotic behavior, fertility, Genetics, QH426-470
Abstract: Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.
Published: 2017
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7. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Author: Julien Boutte, Benoît Aliaga, Oscar Lima, Julie Ferreira de Carvalho, Abdelkader Ainouche, Jiri Macas, Mathieu Rousseau-Gueutin, Olivier Coriton, Malika Ainouche, and Armel Salmon
Subjects: poaceae, duplication, paralogy, polyploidy, bioinformatics, Genetics, QH426-470
Abstract: Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
Published: 2016
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8. Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination

Author: Alexandre Pelé, Mathieu Rousseau-Gueutin, and Anne-Marie Chèvre
Subjects: polyploidy, genome evolution, diploidization, meiosis, unreduced gametes, recombination, Plant culture, SB1-1110
Abstract: Polyploidization is a widespread phenomenon, especially in flowering plants that have all undergone at least one event of whole genome duplication during their evolutionary history. Consequently, a large range of plants, including many of the world’s crops, combines more than two sets of chromosomes originating from the same (autopolyploids) or related species (allopolyploids). Depending on the polyploid formation pathway, different patterns of recombination will be promoted, conditioning the level of heterozygosity. A polyploid population harboring a high level of heterozygosity will produce more genetically diverse progenies. Some of these individuals may show a better adaptability to different ecological niches, increasing their chance for successful establishment through natural selection. Another condition for young polyploids to survive corresponds to the formation of well-balanced gametes, assuring a sufficient level of fertility. In this review, we discuss the consequences of polyploid formation pathways, meiotic behavior and recombination regulation on the speciation success and maintenance of polyploid species.
Published: 2018
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9. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas.

Author: Alexandre Pelé, Matthieu Falque, Gwenn Trotoux, Frédérique Eber, Sylvie Nègre, Marie Gilet, Virginie Huteau, Maryse Lodé, Thibaut Jousseaume, Sylvain Dechaumet, Jérôme Morice, Charles Poncet, Olivier Coriton, Olivier C Martin, Mathieu Rousseau-Gueutin, and Anne-Marie Chèvre
Subjects: Genetics, QH426-470
Abstract: Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.
Published: 2017
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10. I-SceI and customized meganucleases-mediated genome editing in tomato and oilseed rape

Author: Emilie Montes, Maryse Lodé, Benoit Danilo, Anne-Marie Chèvre, Marianne Mazier, Héloïse Archambeau, Mathieu Rousseau-Gueutin, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-11-BTBR-0001,GENIUS,Ingénierie cellulaire : amélioration et innovation technologiques pour les plantes d'une agriculture(2011)
Subjects: Gene Editing, Reporter gene, Transgene, Computational biology, Biology, Tomato, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, chemistry.chemical_compound, Solanum lycopersicum, Genome editing, chemistry, Genes, Reporter, Meganuclease, Genetics, Animal Science and Zoology, Transgenes, Deoxyribonucleases, Type II Site-Specific, Agronomy and Crop Science, Oilseed rape, DNA, Biotechnology, Potential toxicity
Abstract: International audience; Meganucleases are rare cutting enzymes that can generate DNA modifications and are part of the plant genome editing toolkit although they lack versatility. Here, we evaluated the use of two meganucleases, I-SceI and a customized meganuclease, in tomato and oilseed rape. Different strategies were explored for the use of these meganucleases. The activity of a customized and a I-SceI meganucleases was first estimated by the use of a reporter construct GFFP with the target sequences and enabled to demonstrate that both meganucleases can generate double-strand break and HDR mediated recombination in a reporter gene. Interestingly, I-SceI seems to have a higher DSB efficiency than the customized meganuclease: up to 62.5% in tomato and 44.8% in oilseed rape. Secondly, the same exogenous landing pad was introduced in both species. Despite being less efficient compared to I-SceI, the customized meganuclease was able to generate the excision of an exogenous transgene (large deletion of up to 3316 bp) present in tomato. In this paper, we also present some pitfalls to be considered before using meganucleases (e.g., potential toxicity) for plant genome editing.
Published: 2021
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11. Epigenomic and structural events preclude recombination in Brassica napus

Author: Franz Boideau, Gautier Richard, Olivier Coriton, Virginie Huteau, Caroline Belser, Gwenaelle Deniot, Frédérique Eber, Cyril Falentin, Julie Ferreira de Carvalho, Marie Gilet, Maryse Lodé‐Taburel, Loeiz Maillet, Jérôme Morice, Gwenn Trotoux, Jean‐Marc Aury, Anne‐Marie Chèvre, Mathieu Rousseau‐Gueutin, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR‐10‐INBS‐09‐08, Agence Nationale de la Recherche, and SAD18012/00 057661, Région Bretagne
Subjects: Epigenomics, DNA methylation, Physiology, food and beverages, Plant Science, Chromosomes, Plant, brassica napus, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Plant Breeding, recombinaison, oligo-fish, Genome, Plant, In Situ Hybridization, Fluorescence, chromosome inversion
Abstract: International audience; Meiotic recombination is a major evolutionary process generating genetic diversity at each generation in sexual organisms. However, this process is highly regulated, with the majority of crossovers lying in the distal chromosomal regions that harbor low DNA methylation levels. Even in these regions, some islands without recombination remain, for which we investigated the underlying causes.Genetic maps were established in two Brassica napus hybrids to detect the presence of such large nonrecombinant islands. The role played by DNA methylation and structural variations in this local absence of recombination was determined by performing bisulfite sequencing and whole genome comparisons. Inferred structural variations were validated using either optical mapping or oligo fluorescence in situ hybridization.Hypermethylated or inverted regions between Brassica genomes were associated with the absence of recombination. Pairwise comparisons of nine B. napus genome assemblies revealed that such inversions occur frequently and may contain key agronomic genes such as resistance to biotic stresses.We conclude that such islands without recombination can have different origins, such as DNA methylation or structural variations in B. napus. It is thus essential to take into account these features in breeding programs as they may hamper the efficient combination of favorable alleles in elite varieties.
Published: 2022
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12. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Author: Laurie Bertrand, Jean-Marc Aury, Cyril Falentin, Patrick Wincker, Corinne Cruaud, Karine Labadie, Caroline Belser, Benjamin Istace, Anne-Marie Chèvre, Mathieu Rousseau-Gueutin, Loeiz Maillet, Franz Boideau, Gwenaëlle Deniot, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-10-INBS-09–08, Agence Nationale de la Recherche, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, assembly, QH301-705.5, scaffolding, Genomics, Computational biology, Biology, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, chromosome-scale, Brassica rapa, anatomy_morphology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology (General), nanopore, genome, 030304 developmental biology, 0303 health sciences, bionano, General Immunology and Microbiology, plants, Scale (chemistry), Chromosome, Plant genomes, omni-C, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Nanopore, pore-C, Nanopore sequencing, optical map, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.
Published: 2021
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13. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Author: Karine Labadie, Benjamin Istace, Loeiz Maillet, Anne-Marie Chèvre, Gwenaëlle Deniot, Caroline Belser, Jean-Marc Aury, Franz Boideau, Mathieu Rousseau-Gueutin, Corinne Cruaud, Cyril Falentin, Laurie Bertrand, and Patrick Wincker
Subjects: Scale (chemistry), Brassica rapa, Chromosome, Sequence assembly, Genomics, Nanopore sequencing, Computational biology, Biology, Genome, DNA sequencing
Abstract: With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.
Published: 2021
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14. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids

Author: Gwenn Trotoux, Maryse Lodé-Taburel, Jérôme Morice, Mathieu Rousseau-Gueutin, Cyril Falentin, Solenn Stoeckel, Frédérique Eber, Anne-Marie Chèvre, Marie-Madeleine Gilet, Julie Ferreira de Carvalho, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union, a Marie Sklodowska-Curie grant [791908], department 'Biology and Plant Breeding' at INRAE, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Physiology, media_common.quotation_subject, Brassica, Fertility, Plant Science, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Polyploid, Meiosis, homoeologous exchanges, Genetic algorithm, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection (genetic algorithm), polyploidy, 030304 developmental biology, media_common, 2. Zero hunger, fertility, 0303 health sciences, Brassica napus, food and beverages, biology.organism_classification, Aneuploidy, meiotic behavior, Evolutionary biology, euploid selection, Ploidy, Brassica napus (oilseed rape), Genome, Plant, genome stability, 010606 plant biology & botany
Abstract: International audience; Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S-1 to S-9 lineages to explore the positive consequences of euploid selection on B. napus genome stability. Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor. The combined use of both self-fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.
Published: 2021
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15. Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)

Author: Malika L. Aïnouche, Armel Salmon, Delphine Giraud, Mathieu Rousseau-Gueutin, Oscar Lima, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Rennes 1, European UnionEuropean Commission [333709], Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and European Project: 333709,EC:FP7:PEOPLE,FP7-PEOPLE-2012-CIG,GENOMERGE(2013)
Subjects: 0106 biological sciences, 0301 basic medicine, transcriptome evolution, lcsh:QH426-470, Spartina alterniflora, 01 natural sciences, Spartina anglica, allopolyploidy, 03 medical and health sciences, Polyploid, Genetics, hybridization, Genetics (clinical), Original Research, Spartina, biology, Phylogenetic tree, food and beverages, 15. Life on land, biology.organism_classification, Reticulate evolution, Spartina bakeri, transposable elements (TE), lcsh:Genetics, 030104 developmental biology, Evolutionary biology, Chloridoideae, Molecular Medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploidSpartinaspecies (Poaceae, Chloridoideae) that successively diverged in the last 6–10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploidsSpartina alterniflora(2n= 6x= 62) andS. maritima(2n= 6x= 60) that resulted in two sterile F1 hybrids:Spartina×townsendii(2n= 6x= 62) in England andSpartina×neyrautii(2n= 6x= 62) in France. Whole genome duplication ofS.×townsendiigave rise to the invasive neo-allododecaploid speciesSpartina anglica(2n= 12x= 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigatedSpartinaspecies. In 4xand 6xmesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister speciesSpartina bakeriandSpartina versicolor(S. alternifloraandS. maritimathat diverged 2–4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (exceptSINEelements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploidS. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such asS. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.
Published: 2021
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16. Untangling structural factors and evolutionary drivers in nascent polyploids

Author: Anne-Marie Chèvre, Frédérique Eber, Maryse Lodé-Taburel, Gwenn Trotoux, Marie-Madeleine Gilet, Jérôme Morice, Mathieu Rousseau-Gueutin, Solenn Stoeckel, Cyril Falentin, and Julie Ferreira de Carvalho
Subjects: Polyploid, Meiosis, Evolutionary biology, media_common.quotation_subject, Genetic algorithm, Fertility, Outcrossing, Ploidy, Biology, Genome, Selection (genetic algorithm), media_common
Abstract: SUMMARYAllopolyploids have globally higher fitness than their diploid progenitors however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success.Using theBrassicamodel, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploidB. napusand systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors and polyploid formation type. We evaluated the evolution of meiotic behavior, fertility and identified rearrangements in S1 to S9 lineages, to explore the positive consequences of euploid selection onB. napusgenome stability.Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a quasi disappearance of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number strongly depended on the genetic background and cytoplasm donor.The combined use of both self-fertilisation and outcrossing as well as recurrent euploid selection, allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explainB. napusspeciation success.
Published: 2020
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17. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Author: Gwenn Trotoux, Jean-Marc Aury, Loeiz Maillet, Anael Brunet, Franz Boideau, Virginie Huteau, Jérôme Morice, Mathieu Rousseau-Gueutin, Olivier Coriton, Cyril Falentin, Sébastien Letort, Julien Boutte, Maryse Lodé-Taburel, Anne-Marie Chèvre, Gwenaëlle Deniot, Julie Ferreira de Carvalho, Thomas Chaussepied, Caroline Belser, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), H2020 Marie Skłodowska-Curie Actions, Agence Nationale de la Recherche, This work was made possible by financial support of the European Union and a Marie Sklodowska-Curie grant (No. 791908) awarded to JF as well as a BOOST’EUROPE financed by the Conseil régional de Bretagne. FB was supported by a fellowship from BAP INRAE and Conseil régional de Bretagne. This work was additionally supported by the France Génomique National infrastructure, funded as part of the «Investissements d’Avenir » program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: 0106 biological sciences, 0301 basic medicine, Genome evolution, Plant Science, Brassica, Biology, lcsh:Plant culture, genome evolution, 01 natural sciences, Genome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Brassica rapa, lcsh:SB1-1110, Copy-number variation, Genome size, Gene, Comparative genomics, ribosomal DNA, LTR Gypsy, Phenotypic trait, 030104 developmental biology, Evolutionary biology, intraspecific diversity, transposable elements, 010606 plant biology & botany
Abstract: International audience; Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa 'Z1' genome vs. the B. rapa 'Chiifu' genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa 'Z1' and B. rapa 'Chiifu' at the origin of important length differences in some chromosomes. For instance, lengths of 'Z1' and 'Chiifu' A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu.' Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in 'Z1' genome compared to 'Chiifu' on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.
Published: 2020
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18. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Author: Patrick Wincker, Jérémy Lucas, Jean-Marc Aury, Gwenn Trotoux, Anne-Marie Chèvre, Fabrice Legeai, Jérôme Morice, Valérie Barbe, Marie Gilet, Maryse Lodé, Zhesi He, Ian Bancroft, Cyril Falentin, Rod J. Snowdon, Julie Ferreira de Carvalho, Jean Keller, Olivier Filangi, Gwenaëlle Deniot, Mathieu Rousseau-Gueutin, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), University of York [York, UK], Université d'Évry-Val-d'Essonne (UEVE), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), UK Biotechnology and Biological Sciences Research Council. Grant Number: BB/L027844/1Agreenskills+ FellowshipFrance Génomique National infrastructureAgence Nationale pour la Recherche. Grant Number: ANR‐10‐INBS‐09, ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Justus Liebig University, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Justus-Liebig-Universität Gießen = Justus Liebig University (JLU)
Subjects: 0106 biological sciences, 0301 basic medicine, Chloroplasts, Genome, Plastid, interspecific hybridization, Plant Science, Brassica, Biology, 01 natural sciences, Genome, allopolyploidy, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Negative selection, chloroplast, Transcription (biology), Gene Duplication, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene conversion, Plastid, Gene, fungi, Brassica napus, Brassica rapa, duplicated genes, food and beverages, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, genome inheritance, 030104 developmental biology, Paleopolyploidy, intergenomic conflicts, Brassica oleracea, Ploidy, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract: International audience; Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species, can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other one has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared to cytosolic protein complexes and to genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neo-polyploids showed no biased subgenome expression or maternal homogenization via gene conversion despite presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes which could be tested and generalized in other allopolyploid species. This article is protected by copyright. All rights reserved.
Published: 2019
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19. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Author: Caroline Belser, Benjamin Istace, Erwan Denis, Marion Dubarry, Franc-Christophe Baurens, Cyril Falentin, Mathieu Genete, Wahiba Berrabah, Anne-Marie Chèvre, Régine Delourme, Gwenaëlle Deniot, France Denoeud, Philippe Duffé, Stefan Engelen, Arnaud Lemainque, Maria Manzanares-Dauleux, Guillaume Martin, Jérôme Morice, Benjamin Noel, Xavier Vekemans, Angélique D’Hont, Mathieu Rousseau-Gueutin, Valérie Barbe, Corinne Cruaud, Patrick Wincker, Jean-Marc Aury, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Genoscope, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France Genomique : ANR-10-INBS-09-08 Region Hauts-de-France, Ministere de l'Enseignement Superieur et de la Recherche (CPER Climibio), European Fund for Regional Economic Development, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Optics and Photonics, Plant genetics, Plant Science, Computational biology, Brassica, Biology, Chromosome, Genome, Chromosomes, Plant, F30 - Génétique et amélioration des plantes, génomique, 03 medical and health sciences, Nanopores, Polyploid, Séquence d'ADN, ComputingMilieux_MISCELLANEOUS, Genomic organization, Repetitive Sequences, Nucleic Acid, Génome, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Contig, Brassica rapa, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Musa, Brassica campestris, 030104 developmental biology, Minion, Carte génétique, Brassica oleracea, Nanopore sequencing, U30 - Méthodes de recherche, Genome, Plant
Abstract: Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions1–4. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms. Assembling genomes to chromosome scale remains a challenge. Now, a study reports a strategy based on nanopore long reads and optical maps and uses it to produce high-quality chromosome-scale assemblies for the genomes of yellow sarson, broccoli and banana.
Published: 2018
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20. The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants

Author: Jean Keller, Guillaume Martin, Abdelkader Aïnouche, Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Dr. Hamim, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Université de Rennes (UR)
Subjects: 0106 biological sciences, 0301 basic medicine, Nuclear gene, [SDV]Life Sciences [q-bio], InformationSystems_INFORMATIONSTORAGEANDRETRIEVAL, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Viridiplantae, Plastid, plastome evolution, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Genome size, functional gene transfer, endosymbiosis, biology, Archaeplastida, food and beverages, biology.organism_classification, Chloroplast, 030104 developmental biology, Chloroplast DNA, nuclear integrant of plastid DNA (nupt), Evolutionary biology, [SDE]Environmental Sciences, nucleo-cytoplasmic interactions, 010606 plant biology & botany
Abstract: International audience; Photosynthetic eukaryotic cells arose more than a billion years ago through the engulfment of a cyanobacterium that was then converted into a chloroplast, enabling plants to perform photosynthesis. Since this event, chloroplast DNA has been massively transferred to the nucleus, sometimes leading to the creation of novel genes, exons, and regulatory elements. In addition to these evolutionary novelties, most cyanobacterial genes have been relocated into the nucleus, highly reducing the size, gene content, and autonomy of the chloroplast genome. In this chapter, we will first present our current knowledge on the origin and evolution of the plant plastome in the different Archaeplastida lineages (Glaucophyta, Rhodophyta, and Viridiplantae), focusing on its gene content, genome size, and structural evolution. Second, we will present the factors influencing the rate of DNA transfer from the chloroplast to the nucleus, the evolutionary fates of the nuclear integrants of plastid DNA (nupts) in their new eukaryotic environment, and the drivers of chloroplast gene functional relocation to the nucleus. Finally, we will discuss how cytonuclear interactions led to the intertwined coevolution of nuclear and chloroplast genomes and the impact of hybridization and allopolyploidy on cytonuclear interactions
Published: 2018
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21. New insights on homologous recombination in polyploids: the striking case of Brassica allotriploids

Author: Alexandre Pelé, Matthieu Falque, Gwenn Trotoux, Frederique Eber, Sylvie Negre, Marie-Madeleine Gilet, Virginie Huteau, Maryse Lode, Thibaut Jousseaume, Jérôme Morice, Olivier Coriton, Martin, Olivier C., Mathieu Rousseau-Gueutin, Anne-Marie Chèvre, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, crossover, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, allotriploid hybrids, homologous recombination, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Brassica
Abstract: National audience; Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. While one obligate CO occurs per pair of homologs, ensuring their proper segregation during meiosis, rarely more than three are formed and their distribution is not homogenous along chromosomes. In plants, Whole Genome Duplication (WGD) was highlighted to result in a boost of the number of COs between homologous chromosomes, which may contribute to the success of allopolyploid species by generating enhanced allelic combinations. However, the consequences on COs distribution as well as the regulation of this phenomenon are poorly understood. We investigated here the striking case of Brassica allotriploids (AAC, 2n=3x=29), resulting from crosses between B. napus (AACC, 2n=4x=38) and its B. rapa progenitor (AA, 2n=2x=20), showing far higher CO rates between A homologs than diploids and allotetraploids due to specific additional C chromosomes. From several populations developed, we assessed the homologous recombination in AA diploids and hybrids carrying either an additional complete C genome (9 C chromosomes) or specific C chromosomes, through the genotyping of 204 SNP markers well distributed along A chromosomes (one SNP each 1.2 Mb). Compared to what was previously known, we showed that the presence of the C genome in AAC allotriploids leads to a very substantial increase of COs all along the A chromosomes, especially in the vicinity of centromeres that are normally deprived of COs. We also demonstrated that the addition of a C09 chromosome originating either from B. oleracea (CC, 2n=2x=18) or B. napus have contrasted effects on recombination. This latter result points out that regulation of homologous recombination in AAC allotriploids may have changed in the allopolyploid B. napus, as a result of the 7,500 years of genome coevolution in a polyploid context. Together, our findings provide new insights on homologous recombination in allopolyploids as well as the opportunity to break the linkage disequilibrium in the rapeseed breading programs by using allotriploids.
Published: 2017

22. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

Author: Charles Poncet, Frédérique Eber, Mathieu Rousseau-Gueutin, Jérôme Morice, Alexandre Pelé, Sylvain Dechaumet, Gwenn Trotoux, Anne-Marie Chèvre, Maryse Lodé, Virginie Huteau, Thibaut Jousseaume, Sylvie Negre, Marie Gilet, Matthieu Falque, Olivier Coriton, Olivier C. Martin, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Conseil Régional de Bretagne, BAP INRA, BAP INRA Département, ANR-14-CE19-0004,CROC,Contrôle de la fréquence de recombinaison méiotique pour accélérer l'innovation variétales chez les espèces cultivées polyploïdes(2014), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), ANR- 14-CE19-0004, ANR, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0301 basic medicine, Cancer Research, [SDV]Life Sciences [q-bio], Interference (genetic), Biochemistry, Chromosomal crossover, Homologous Chromosomes, recombinaison méiotique, chromosome, Cell Cycle and Cell Division, Crossing Over, Genetic, Homologous Recombination, Genetics (clinical), Genetic Interference, Genetics, Recombination, Genetic, education.field_of_study, Chromosome Biology, Chromosome Mapping, genêtic variation, Nucleic acids, Meiosis, Cell Processes, diversité génétique, Ploidy, Genome, Plant, Research Article, lcsh:QH426-470, DNA recombination, Population, crossing over, Brassica, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, Chromosomes, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Polyploidy, 03 medical and health sciences, Genetic variation, education, Molecular Biology Techniques, genome, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Hybrid, génome, Gene Mapping, Chromosome, Biology and Life Sciences, Genetic Variation, Cell Biology, DNA, Chromosome Pairs, lcsh:Genetics, 030104 developmental biology
Abstract: Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs., Author summary In organisms with sexual reproduction, meiosis generates gametes containing half of the genetic material of parents. During this process, the reciprocal exchanges between the homologous chromosomes due to crossovers (COs) ensure their proper segregation as well as the generation of diversity. However, the number of COs is limited and their location is heterogeneous along chromosomes. A major challenge is to overcome these constraints for enhancing the genetic shuffling of alleles. This work demonstrates that it is possible to do so in Brassica hybrids obtained by manual crossings, combining a complete set of homologous chromosomes and a haploid set provided by a related species. Specifically, by studying large segregating populations, we find that in allotriploid Brassica hybrids, more COs are formed all along the homologous chromosomes, especially in regions usually deprived of COs, compared to diploids. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of new diversity.
Published: 2017
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23. The impact of open pollination on the structural evolutionary dynamics, meiotic behavior, and fertility of resynthesized allotetraploid Brassica napus L

Author: Virginie Huteau, Gwenn Trotoux, Olivier Coriton, Sylvie Negre, Mathieu Rousseau-Gueutin, Marie Gilet, Sonia Vautrin, Jérôme Morice, Cyril Falentin, Alexandre Pelé, Maryse Lodé, Frédérique Eber, Anne-Marie Chèvre, Hélène Bergès, Joëlle Fourment, Gwennaëlle Deniot, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), ANR-10-EQPX-07-01, ERA-CAPS13.017_Evo-Genapus, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0301 basic medicine, Genomics, QH426-470, Biology, Brassica napus, allopolyploidy, genome dynamic, meiotic behavior, fertility, Genome, méïose, brassica napus, Open pollination, 03 medical and health sciences, Meiosis, Polyploid, polyploïdie, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Genome size, Genetics (clinical), polyploidy, Vegetal Biology, Selfing, Chromosome, food and beverages, 030104 developmental biology, diversité allélique, plante à fleurs, hybridation génomique in situ, Biologie végétale, allopolyploidie
Abstract: Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.
Published: 2017
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24. Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Author: Christian Obermeier, Sarah Schiessl, Anne-Marie Chèvre, Rod J. Snowdon, Isobel A. P. Parkin, Anna Stein, Mathieu Rousseau-Gueutin, Birgit Samans, Olivier Coriton, Justus-Liebig-Universität Gießen (JLU), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Agriculture and Agri-Food [Ottawa] (AAFC), SN 14/17-1, ERA-CAPS, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Agriculture and Agri-Food (AAFC), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Candidate gene, Chromosomes, Artificial, Bacterial, carte génétique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Genetic Linkage, [SDV]Life Sciences [q-bio], Genome rearrangements, Plant Science, 01 natural sciences, single nucleotide polymorphism, Copy-number variation, mapping, Research Articles, In Situ Hybridization, Fluorescence, Genetics, Gene Rearrangement, Recombination, Genetic, education.field_of_study, qtl, Chromosome Mapping, Nucleic Acid Hybridization, food and beverages, Phenotype, Seeds, genetic mapping, Genome, Plant, Biotechnology, Research Article, DNA Copy Number Variations, DNA, Plant, Genotype, analyse cytogénétique, Population, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Chromosomes, Plant, brassica napus, 03 medical and health sciences, Gene mapping, Genetic linkage, homoeologous exchange, education, Bacterial artificial chromosome, Whole Genome Sequencing, génome, quantitative trait loci, réarrangement génomique, Gene rearrangement, Diploidy, échange génique, Chromosome Pairing, 030104 developmental biology, genetic, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high-density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole-genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC-FISH) coupled with PCR using primers specific to the rearranged region. Using a well-known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.
Published: 2017
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25. Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus - Raphanus raphanistrum Model

Author: Bachar Alrustom, Virginie Huteau, Jérôme Morice, Henri Darmency, Maryse Lodé, Katarzyna Adamczyk-Chauvat, Gwenaëlle Thomas, Frédérique Eber, Anne-Marie Chèvre, Sabrina Delaunay, Mathieu Rousseau-Gueutin, Cyril Falentin, Olivier Coriton, Eric Jenczewski, Caroline François, Sylvie Negre, Marie Gilet, Anne Vannier, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, SAD Paysage (SAD Paysage), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] ( MaIAGE ), Institut National de la Recherche Agronomique ( INRA ), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères ( P3F ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, SAD Paysage ( SAD Paysage ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0301 basic medicine, oilseed rape, [SDV]Life Sciences [q-bio], Brassica, introgression, Introgression, Plant Weeds, Investigations, Raphanus raphanistrum, Genes, Plant, Genome, Gene flow, Raphanus, 03 medical and health sciences, Botany, Genetics, Gene, Hybrid, intergeneric hybridization, 2. Zero hunger, biology, [ SDV ] Life Sciences [q-bio], food and beverages, 15. Life on land, biology.organism_classification, 030104 developmental biology, Hybridization, Genetic, wild radish, Genetic Fitness, Weed
Abstract: The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties (Brassica napus, AACC, 2n = 38) by a local population of wild radish (Raphanus raphanistrum, RrRr, 2n = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0–28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow.
Published: 2017
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26. The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate

Author: Alexandre Pelé, Cyril Falentin, Mathieu Rousseau-Gueutin, Sylvie Negre, Marie Gilet, Gwenn Trotoux, Jérôme Morice, Gwenaëlle Deniot, Anne-Marie Chèvre, Frédérique Eber, Maryse Lodé, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Chercheur indépendant, BAP INRA, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, 0301 basic medicine, oilseed rape, Physiology, [SDV]Life Sciences [q-bio], Introgression, Genomics, Context (language use), Plant Science, Biology, 01 natural sciences, Genome, Chromosomes, Plant, allopolyploidy, brassica napus, Polyploidy, 03 medical and health sciences, Polyploid, evolution, Gene, Genetics, génome, subgenome extraction, alloploidy, food and beverages, Biological Evolution, Diploidy, 030104 developmental biology, Genetic marker, évolution du génome, Hybridization, Genetic, Pollen, structural rearrangements, Ploidy, Genome, Plant, alloploidie, 010606 plant biology & botany
Abstract: International audience; Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.
Published: 2017
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27. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

Author: Solenn Cordonnier, Oscar Lima, Armel Salmon, Sophie Michon-Coudouel, Julie Ferreira de Carvalho, Abdelkader Aïnouche, Guillaume Martin, Malika L. Aïnouche, Mathieu Rousseau-Gueutin, Delphine Naquin, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Plateforme Génomique Environnementale et Fonctionnelle (GEF), Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Bretagne, grant no. 333709, European Project, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, Phylogénie, repeated plastid sequences, Lineage (evolution), Plant Science, Polymerase Chain Reaction, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Lupinus luteus, Lupinus, sequence divergence, Chloroplaste, European yellow lupine, Phylogeny, functional gene transfer, Genetics, Papilionoidae, 0303 health sciences, biology, chloroplast genome evolution, Fabaceae, legume, Genistoid clade, 36-kb inversion, Chloroplast DNA, plastome hotspots, Séquence nucléotidique, structural plastid rearrangement, F60 - Physiologie et biochimie végétale, Molecular Sequence Data, 010603 evolutionary biology, Fabaceae phylogeny, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, lineage-specific marker, food, Phylogenetics, Plastid, Genome, Chloroplast, Transfert de gène, 030304 developmental biology, Génome, Sequence Analysis, DNA, Original Articles, flip-flop recombination, biology.organism_classification, food.food, Acide aminé, inverted repeats
Abstract: support from the 'Plate-forme Génomique Environnementale et Fonctionnelle' (OSUR: INEE-CNRS) and the Genouest Bioinformatic Plateform (University of Rennes 1); International audience; † Background and Aims To date chloroplast genomes are available only for members of the non-protein amino acidaccumulating clade (NPAAA) Papilionoid lineages in the legume family (i.e. Millettioids, Robinoids and the 'inverted repeat-lacking clade', IRLC). It is thus very important to sequence plastomes from other lineages in order to better understand the unusual evolution observed in this model flowering plant family. To this end, the plastome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group. † Methods The plastome of L. luteus was reconstructed using Roche-454 and Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other Fabaceae plastomes. PCR screening and sequencing were performed in other allied legumes in order to determine the origin of a large inversion identified in L. luteus. † Key Results The first sequenced Genistoid plastome (L. luteus: 155 894 bp) resulted in the discovery of a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy (LSC) region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most probably resulted from a flip-flop recombination between identical 29-bp inverted repeats within two trnS genes. Comparative analyses of the chloroplast gene content of L. luteus vs. Fabaceae and extra-Fabales plastomes revealed the loss of the plastid rpl22 gene, and its functional relocation to the nucleus was verified using lupine transcriptomic data. An investigation into the evolutionary rate of coding and non-coding sequencesamong legume plastomes resulted in the identification of remarkably variable regions. †Conclusions This study resulted in the discovery of a novel, major 36-kb inversion, specific to the Genistoids. Chloroplast mutational hotspots were also identified, which contain novel and potentially informative regions for molecular evolutionary studies at various taxonomic levels in the legumes. Taken together, the results provide new insights into the evolutionary landscape of the legume plastome.
Published: 2014
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28. The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized Allotetraploid

Author: Mathieu, Rousseau-Gueutin, Jérôme, Morice, Olivier, Coriton, Virginie, Huteau, Gwenn, Trotoux, Sylvie, Nègre, Cyril, Falentin, Gwennaëlle, Deniot, Marie, Gilet, Frédérique, Eber, Alexandre, Pelé, Sonia, Vautrin, Joëlle, Fourment, Maryse, Lodé, Hélène, Bergès, and Anne-Marie, Chèvre
Subjects: fertility, Brassica napus, food and beverages, Investigations, Chromosomes, Plant, allopolyploidy, Evolution, Molecular, Polyploidy, Meiosis, genome dynamic, meiotic behavior, Hybridization, Genetic, Pollination, Genome, Plant, In Situ Hybridization, Fluorescence
Abstract: Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.
Published: 2016

29. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Author: Malika L. Aïnouche, Julien Boutte, Mathieu Rousseau-Gueutin, Corinne Da Silva, Patrick Wincker, Armel Salmon, Julie Ferreira de Carvalho, Julie Poulain, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), LIA Ecological Genomics of Polyploidy, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Salmon, Armel
Subjects: 0301 basic medicine, homeo-SNPs, transcriptome de novo assembly, K-S distribution, polyploidy, haplotyping, paralogs-orthologs-homeologs, Genotyping Techniques, Genomics, Biology, Poaceae, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, paralogs–orthologs–homeologs, Gene Duplication, Gene duplication, Genetics, KS distribution, Ecology, Evolution, Behavior and Systematics, Gene Library, Spartina, Haplotype, food and beverages, Reference Standards, biology.organism_classification, 030104 developmental biology, Haplotypes, Ploidy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Synonymous substitution, Transcriptome, Reference genome, Research Article
Abstract: International audience; In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica. These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.
Published: 2016
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30. Unending hybridization and polyploid speciation stories: Lessons from Spartina (Poaceae)

Author: Aïnouche, Malika L., Alex Baumel, Blanca Gallego-Tévar, Jesus Castillo, Mathieu Rousseau-Gueutin, Julien Boutte, Julie Ferreira de Carvalho, Houda Chelaifa, Oscar Lima, Ales Kovarik, Andrew Leitch, Ilia Leitch, Abdelkhader Ainouche, Armel Salmon, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Universidad de Sevilla / University of Sevilla, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Inst Biophys, Vvi, CZ-61265 Brno, Czech Academy of Sciences [Prague] (CAS), Sch Biol & Chem Sci, Queen Mary University of London (QMUL), Organization for the Phyto-Taxonomic Investigation of the Mediterranean Area, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universidad de Sevilla, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Czech Academy of Sciences [Prague] (ASCR), Briand, Valerie, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

31. Blueberry

Author: Mathieu Rousseau-gueutin
Published: 2016
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32. Spartina versicolor Fabre: Another case of Spartina trans-Atlantic introduction?

Author: Hélène Rousseau, Mathieu Rousseau-Gueutin, N. Duong, Agnès Gareil, C. Sapienza-Bianchi, Olivier Coriton, Malika L. Aïnouche, Saverio Sciandrello, Rachid Amirouche, Alex Baumel, Isabel Caçador, Bernardo Duarte, Jose M. del Castillo, Aix Marseille Université (AMU), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Université de Rennes (UNIV-RENNES), Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), Università degli Studi di Catania (UniCT), University of Lisbon, University Seville, Biological Invasion Programm of UMR-CNRS Ecobio (University of Rennes 1), LIA ECOGEN, Partner University Funds, Financial support from the Region Bretagne, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Sevilla, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR), Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Università degli studi di Catania = University of Catania (Unict), Universidade de Lisboa = University of Lisbon (ULISBOA), Universidad de Sevilla / University of Sevilla, and Repositório da Universidade de Lisboa
Subjects: 0106 biological sciences, 0301 basic medicine, Cordgrass, Mediterranean, 010603 evolutionary biology, 01 natural sciences, Invasive species, Genetic diversity, Spartina patens, Species status, 03 medical and health sciences, Genus, 14. Life underwater, Microsatellites, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics, Phylogeny, Spartina, Ecology, biology, Cordgrass, Genetic diversity, Species status, Mediterranean, Microsatellites, Phylogeny, 15. Life on land, biology.organism_classification, 030104 developmental biology, Herbarium, Gene pool, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Intercontinental introductions are widespread in the genus Spartina, with important ecological and evolutionary consequences. The native or introduced status of Spartina species is then critical with regard to biodiversity assessment, especially for vulnerable Mediterranean coastline ecosystems. Spartina versicolor was first recorded in southern France in 1849, then successively in various places on the European and North-African Mediterranean and Atlantic coasts. This species is considered to be either a European native or an invasive species introduced from North America which has a high morphological similarity to the Atlantic American species Spartina patens. We performed extensive sampling of S. versicolor in Europe and North Africa (from natural populations and herbarium collections) and compared these samples to other European and American Spartina species (including S. patens). Chromosome counts were reported for the first time and revealed that S. versicolor is tetraploid (2n = 4x = 40). Phylogenetic analyses based on chloroplast and nuclear ribosomal DNA sequences did not reveal any molecular variation within S. versicolor. In this species, a single haplotype, that is identical to one haplotype of S. patens, was found in the four chloroplast and the nuclear ribosomal ITS regions investigated. In addition, simple sequence repeat markers were used and revealed a low level of genetic diversity within S. versicolor, suggesting that the introduction of S. versicolor occurred from a narrow genetic pool of S. patens from North Americ
Published: 2016
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33. Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

Author: Philipp E. Bayer, Jérôme Morice, Matthew N. Nelson, Anne-Marie Chèvre, Jacqueline Batley, Anouska Cousin, Naghmeh Besharat, A. Pradhan, Isobel A. P. Parkin, Mathieu Rousseau-Gueutin, Annaliese S. Mason, Justus-Liebig-Universität Gießen (JLU), University of Queensland (UQ), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), The University of Western Australia (UWA), Agriculture and Agri-Food [Ottawa] (AAFC), University of Southern Queensland (USQ), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Agriculture and Agri-Food (AAFC)
Subjects: Genetic Markers, 0106 biological sciences, 0301 basic medicine, Genotyping Techniques, Centromere, Sequence assembly, Genomics, molecular karyotyping, Brassica, Investigations, Biology, Genes, Plant, Polymorphism, Single Nucleotide, 01 natural sciences, Genome, 03 medical and health sciences, Gene mapping, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, unreduced gametes, Gene, Crosses, Genetic, Repetitive Sequences, Nucleic Acid, fungi, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, centromeres, recombination, 030104 developmental biology, Haplotypes, Genetic marker, DNA Transposable Elements, Genome, Plant, 010606 plant biology & botany, Reference genome
Abstract: Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.
Published: 2016
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34. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

Author: Jérôme Morice, Christine Bissuel-Belaygue, Mathieu Rousseau-Gueutin, Olivier Maes, Jean-Eric Dheu, Pierre George, Florent Guinot, Anne-Sophie Bouchet, Xavier Pinochet, Damien Dugué, Cécile Baron, Nathalie Nesi, Anne Laperche, Thomas Foubert, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Groupe Limagrain, Biogemma, Terres Inovia, Euralis Semences, Maïsadour Semences, Rouergue Auvergne Gévaudan Tarnais, Syngenta, French National Research Agency (ANR) [ANR-07-GPLA-016], program 'Investments for the Future' [ANR-11-BTBR-0004], Ministere de l'Enseignement Superieur et de la Recherche, Laperche, Anne, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and ANR-11-BTBR-0004,RAPSODYN,Optimisation de la teneur et du rendement en huile chez le colza cultivé sous contrainte azotée(2011)
Subjects: 0106 biological sciences, 0301 basic medicine, Rapeseed, Genetic Linkage, [SDV]Life Sciences [q-bio], 01 natural sciences, Cluster Analysis, Genetics(clinical), Gene–environment interaction, Genetics (clinical), 2. Zero hunger, Brassica rapa, Chromosome Mapping, Genomics, Biological Evolution, Trait, Seasons, Algorithms, Genome, Plant, Research Article, Quantitative trait loci, Nitrogen stress, Genotype, Ecovalence, Nitrogen, Growing season, Biology, Quantitative trait locus, Brassica napus L, Genotype x nitrogen interactions, 03 medical and health sciences, Quantitative Trait, Heritable, Genotype × nitrogen interactions, Genetics, Genetic Association Studies, Genetic association, Models, Statistical, business.industry, Crop yield, 15. Life on land, Biotechnology, 030104 developmental biology, Agronomy, Gene-Environment Interaction, business, Energy Metabolism, 010606 plant biology & botany, Genome-Wide Association Study
Abstract: Background Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Results Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Conclusions Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition levels on seed yield-related traits under our experimental conditions. Nevertheless, critical genomic regions associated with yield that were stable across environments were identified in rapeseed. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0432-z) contains supplementary material, which is available to authorized users.
Published: 2016
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35. Plastid Sequences Contribute to Some Plant Mitochondrial Genes

Author: Dong Wang, Jeremy N. Timmis, Mathieu Rousseau-Gueutin, and University of Adelaide
Subjects: 0106 biological sciences, Mitochondrial DNA, Molecular Sequence Data, Gene Conversion, Biology, Mitochondrion, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Genetics, Posttranscriptional RNA processing, Plastids, Gene conversion, Plastid, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Base Sequence, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, food and beverages, Genes, Mitochondrial, Transfer RNA, 010606 plant biology & botany
Abstract: DNA of plastid (chloroplast) origin comprises between 1% and 10% of the mitochondrial genomes of higher plants, but functions are currently considered to be limited to rare instances where plastid tRNA genes have replaced their mitochondrial counterparts, where short patches of mitochondrial genes evolved using their homologous plastidic copies by gene conversion or where a new promoter region is created. Here, we show that, in some angiosperms, plastid-derived DNA in mitochondrial genomes (also called mtpt for mitochondrial plastid DNA) contributes codons to unrelated mitochondrial protein-coding sequences and may also have a role in posttranscriptional RNA processing. We determined that these transfers of plastid DNA occurred a few to 150 Ma and that mtpts can sometimes remain dormant many millions of years before contributing to the mitochondrial proteome.
Published: 2012
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36. A novel class of PTEN protein in Arabidopsis displays unusual phosphoinositide phosphatase activity and efficiently binds phosphatidic acid

Author: Jérôme Joubès, Rodnay Sormani, Christa Testerink, Michel Castroviejo, Véronique Germain, Anne Pribat, Christian Meyer, Mathieu Rousseau-Gueutin, Michel Laguerre, Magdalena M. Julkowska, Christophe Rothan, Plant Physiology (SILS, FNWI), Green Life Sciences, and Université Sciences et Technologies - Bordeaux 1
Subjects: Models, Molecular, 0106 biological sciences, Protein Conformation, Phosphatase, Arabidopsis, Phosphatidic Acids, Protein tyrosine phosphatase, 01 natural sciences, Biochemistry, Expression in planta, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Phosphatidic acid (PA) binding, Escherichia coli, PTEN, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Phylogeny, 030304 developmental biology, 0303 health sciences, Site-directed mutagenesis, biology, Arabidopsis Proteins, Effector, PTEN Phosphohydrolase, Life Sciences, Cell Biology, Phosphatidic acid, Lipid signaling, biology.organism_classification, Phosphoric Monoester Hydrolases, Phosphoinositide phosphatase, Phylogenetics, chemistry, biology.protein, Signal transduction, Protein Binding, Signal Transduction, 010606 plant biology & botany
Abstract: PTEN (phosphatase and tensin homologue deleted on chromosome ten) proteins are dual phosphatases with both protein and phosphoinositide phosphatase activity. They modulate signalling pathways controlling growth, metabolism and apoptosis in animals and are implied in several human diseases. In the present paper we describe a novel class of PTEN pro-teins in plants, termed PTEN2, which comprises the AtPTEN (Arabidopsis PTEN) 2a and AtPTEN2b proteins in Arabidopsis. Both display low in vitro tyrosine phosphatase activity. In addition, AtPTEN2a actively dephosphorylates in vitro the 3′ phosphate group of PI3P (phosphatidylinositol 3-phosphate), PI(3,4)P2 (phosphatidylinositol 3,4-bisphosphate) and PI(3,5)P2 (phosphatidylinositol 3,5-bisphosphate). In contrast with animal PTENs, PI(3,4,5)P3 (phosphatidylinositol 3,4,5-trisphosphate) is a poor substrate. Site-directed mutagenesis of AtPTEN2a and molecular modelling of protein–phosphoinositide interactions indicated that substitutions at the PTEN2 core catalytic site of the Lys267 and Gly268 residues found in animals, which are critical for animal PTEN activity, by Met267 and Ala268 found in the eudicot PTEN2 are responsible for changes in substrate specificity. Remarkably, the AtPTEN2a protein also displays strong binding activity for PA (phosphatidic acid), a major lipid second messenger in plants. Promoter::GUS (β-glucuronidase) fusion, transcript and protein analyses further showed the transcriptional regulation of the ubiquitously expressed AtPTEN2a and AtPTEN2b by salt and osmotic stress. The results of the present study suggest a function for this novel class of plant PTEN proteins as an effector of lipid signalling in plants.
Published: 2012
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37. Development, mapping and transferability of Fragaria EST-SSRs within the Rosodae supertribe

Author: Mathieu Rousseau-Gueutin, Beatrice Denoyes-Rothan, H. Caron, Loïck Le Dantec, and L. Richard
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Expressed sequence tag, Plant Science, Biology, Fragaria, 01 natural sciences, 03 medical and health sciences, Polyploid, Gene mapping, Genetic marker, Microsatellite, Ploidy, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany, Synteny
Abstract: With 1 figure and 3 tables Abstract The Rosodae supertribe is composed of economically important species (strawberry, rose and raspberry). In order to extend the repertoire of markers for optimizing genetic mapping and synteny within this supertribe, we developed 20 functional markers from two Fragaria cDNA libraries enriched in AG/AC microsatellite motifs. We tested their transferability within the Rosodae supertribe, including two reference diploid and octoploid strawberry segregating populations. Out of these 20 functional markers, 70% revealed polymorphism in both diploid and octoploid Fragaria segregating populations and were mapped on the diploid genetic map to provide useful information for further marker-assisted selection. These 20 EST-SSRs were also tested in 17 wild Fragaria species and displayed a high cross-species transferability (mean of 95%), providing new markers for further diversity studies within the genus. These markers were also transferable to the phylogenetically close Potentilla genus, whereas their transferability was lower for the polyploid Duchesnea indica species and for the more distant Rosa genus. Their use for genetic mapping within the Rosodae will further permit a comparison of genetic information among the different genera.
Published: 2011
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38. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Author: Malika L. Aïnouche, Benoît Aliaga, Armel Salmon, Abdelkader Aïnouche, Mathieu Rousseau-Gueutin, Jiri Macas, Oscar Lima, Julien Boutte, Julie Ferreira de Carvalho, Olivier Coriton, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Inst Plant Mol Biol, Ctr Biol, Czech Academy of Sciences [Prague] (CAS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), nternational Associated Laboratory 'Ecological Genomics of Polyploidy' - CNRS (INEE) [UMR CNRS 6553 Ecobio], University of Rennes 1, Iowa State University (Ames, USA), Partner University Funds, Molecular Ecology Platform [UMR CNRS 6553, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (ASCR), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Genomics, QH426-470, Biology, Investigations, Genes, Plant, Genome, DNA, Ribosomal, Polymorphism, Single Nucleotide, DNA sequencing, Polyploidy, 03 medical and health sciences, Open Reading Frames, Genetics, Coding region, Molecular Biology, Gene, paralogy, Genetics (clinical), In Situ Hybridization, Fluorescence, Phylogeny, poaceae, duplication, polyploidy, bioinformatics, Haplotype, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Molecular Sequence Annotation, External transcribed spacer, 030104 developmental biology, Haplotypes, RNA, Ribosomal, Ploidy, Genome, Plant
Abstract: Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
Published: 2015
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39. A tale of two spartinas: Climatic, photobiological and isotopic insights on the fitness of non-indigenous versus native species

Author: João Carlos Marques, Isabel Caçador, Bernado Duarte, Alexandra Baeta, Malika L. Aïnouche, Mathieu Rousseau-Gueutin, Marine and Environmental Sciences Centre (MARE), Faculdade de Ciencias da Universidade de Lisboa, Marine and environmental research centre - IMAR-CMA (Coimbra, Portugal), University of Coimbra [Portugal] (UC), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), The authors would like to thank to the 'Fundação para a Ciência e Tecnologia (FCT)' for funding the research in the Marine and Environmental Sciences Centre (MARE) throughout the project UID/MAR/04292/2013 and this specific work throughout the ECOSAM project (PTDC/AAC-CLI/104085/2008). B. Duarte investigation was supported by FCT throughout a PhD grant (SFRH/BD/75951/2011) and throughout the COST action TD1209 (COST-STSM-TD1209-16451)., Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Repositório da Universidade de Lisboa
Subjects: 0106 biological sciences, Mediterranean climate, Marsh, 010504 meteorology & atmospheric sciences, Ecophysiological fitness, Aquatic Science, Oceanography, 01 natural sciences, S. maritima, Botany, Photosynthesis, 0105 earth and related environmental sciences, Abiotic component, N nutrition, Spartina, geography, Biomass (ecology), geography.geographical_feature_category, biology, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, biology.organism_classification, Salinity, Productivity (ecology), S. versicolor, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Spartina maritima
Abstract: International audience; Salt marshes are facing a new threat: the invasion by non-indigenous species (NIS), Although its introduction time is not established yet, in 1999 Spartina versicolor was already identified as a NIS in the Mediterranean marshes, significantly spreading its area of colonization. Using the Mediterranean native Spartina maritima as a reference, the present research studied the ecophysiological fitness of this NIS in its new environment, as a tool to understand its potential invasiveness. It was found that Spartina versicolor had a stable photobiological pattern, with only minor fluctuations during an annual cycle, and lower efficiencies comparated to S. maritima. The NIS seems to be rather insensitive to the observed abiotic factors fluctuations (salinity and pH of the sediment), and thus contrasts with the native S. maritima, known to be salinity dependent with higher productivity values in higher salinity environments. Most of the differences observed between the photobiology of these species could be explained by their nitrogen nutrition (here evaluated by the δ15N stable isotope) and directly related with the Mediterranean climate. Enhanced by a higher N availability during winter, the primary production of S. maritima which lead to dilution of the foliar δ15N concentration in the newly formed biomass, similarly to what is observed along a rainfall gradient. On the other hand, S. versicolor showed an increased δ15N in its tissues along the annual rainfall gradient, probably due to a δ15N concentration effect during low biomass production periods (winter and autumn). Together with the photobiological traits, these isotopic data point out to a climatic misfit of S. versicolor to the Mediterranean climate compared to the native S. maritima. This appears to be the major constrain shaping the ecophysiological fitness of this NIS, its primary production and consequently, its spreading rate along the Mediterranean marshes.
Published: 2015
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40. Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family

Author: Carine Charron, Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Houda Chelaifa, Julien Boutte, Droc, G., Fourment, J., Bellec, A., Berges, H., Poulain, J., Couloux, A., Mangenot, S., Wincker, P., Armel Salmon, Angélique Dhont, Malika Ainouche, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, UMR CNRS 6553 ECOBIO, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: F70 - Taxonomie végétale et phytogéographie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, F30 - Génétique et amélioration des plantes
Abstract: International audience
Published: 2014

41. Recurrent polyploidy in the salt marsh genus Spartina: Lessons and challenges

Author: Malika Ainouche, Julie Ferreira de Carvalho, Julien Boutte, Sidonie Bellot, Mathieu Rousseau-Gueutin, Abdelkader Aïnouche, Carine Charron, Angélique Dhont, Andrew Leitch, Ales Kovarik, Armel Salmon, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Sch Biol & Chem Sci, Queen Mary University of London (QMUL), Inst Biophys, VVI, Czech Academy of Sciences [Prague] (CAS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Czech Academy of Sciences [Prague] (ASCR), and Briand, Valerie
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2014

42. Potential Functional Replacement of the Plastidic Acetyl-CoA Carboxylase Subunit (accD) Gene by Recent Transfers to the Nucleus in Some Angiosperm Lineages

Author: Xun Huang, Michael Ayliffe, Mathieu Rousseau-Gueutin, Jeremy N. Timmis, Emily Higginson, Anil Day, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Adelaide, Faculty of Life Sciences [Manchester], University of Manchester [Manchester], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Nuclear gene, Physiology, Protein subunit, fungi, Acetyl-CoA carboxylase, food and beverages, Plant Science, Biology, 01 natural sciences, Chloroplast, 03 medical and health sciences, Chloroplast DNA, Coding region, Plastid, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic acetyl-CoA carboxylase subunit (accD) gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to green fluorescent protein was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified, and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.
Published: 2013
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43. PFRU, a single dominant locus regulates the balance between sexual and asexual plant reproduction in cultivated strawberry

Author: Amèlia Gaston, Justine Perrotte, Christophe Rothan, E. Lerceteau-Köhler, Michel Hernould, Mathieu Rousseau-Gueutin, Béatrice Denoyes, Aurélie Petit, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Swedish University of Agricultural Sciences (SLU), Region Aquitaine, EU FP7-KBBE-2010-4 Project [265942], Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, genetic control, Perennial plant, Physiology, QTL, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Population, Locus (genetics), Plant Science, Biology, Quantitative trait locus, Fragaria, 01 natural sciences, Plant reproduction, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, sexual and asexual reproduction, perpetual flowering, education, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, 0303 health sciences, education.field_of_study, Reproduction, Stolon, fungi, food and beverages, Inflorescence, runnering, strawberry, human activities, 010606 plant biology & botany
Abstract: International audience; Strawberry (Fragaria sp.) stands as an interesting model for studying flowering behaviour and its relationship with asexual plant reproduction in polycarpic perennial plants. Strawberry produces both inflorescences and stolons (also called runners), which are lateral stems growing at the soil surface and producing new clone plants. In this study, the flowering and runnering behaviour of two cultivated octoploid strawberry (Fragaria×ananassa Duch., 2n=8×=56) genotypes, a seasonal flowering genotype CF1116 and a perpetual flowering genotype Capitola, were studied along the growing season. The genetic bases of the perpetual flowering and runnering traits were investigated further using a pseudo full-sibling F1 population issued from a cross between these two genotypes. The results showed that a single major quantitative trait locus (QTL) named FaPFRU controlled both traits in the cultivated octoploid strawberry. This locus was not orthologous to the loci affecting perpetual flowering (SFL) and runnering (R) in Fragaria vesca, therefore suggesting different genetic control of perpetual flowering and runnering in the diploid and octoploid Fragaria spp. Furthermore, the FaPFRU QTL displayed opposite effects on flowering (positive effect) and on runnering (negative effect), indicating that both traits share common physiological control. These results suggest that this locus plays a major role in strawberry plant fitness by controlling the balance between sexual and asexual plant reproduction.
Published: 2013
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44. Gene Transfer to the Nucleus

Author: Jeremy N. Timmis, Anna E. Sheppard, Mathieu Rousseau-Gueutin, Andrew H. Lloyd, University of Adelaide, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and C.E. Bullerwell
Subjects: Proteomics, 0303 health sciences, Mitochondrial DNA, Nuclear gene, Endosymbiosis, [SDV]Life Sciences [q-bio], Genomics, Biology, Genome, Chloroplast, Mitochondria, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Evolutionary biology, Organelle, medicine, Nuclear protein, Nucleus, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: The endosymbiotic evolution of mitochondrial and plastid genomes from ancestral prokaryotes is outlined stressing the net passage of genes from the organelle precursor genomes to the nucleus. We highlight recent experimental analyses of the process of nucleic acid transfer between extant organelle genomes and the nucleus. The molecular events that have accompanied functional gene transfers are described and specific cases of the relocation and nuclear expression of former organellar genes are summarised. The mechanisms underpinning gene transfer, including the movement of extant cytoplasmic organellar nucleic acids are described together with emphasis on the genetic consequences for the nuclear size and genetic complexity. We discuss the major contribution of endosymbiosis to the evolution of eukaryotes and we mention the selective forces that may be responsible for making the nucleus the preferred location for eukaryotic genes.
Published: 2012
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45. Plastid DNA in the nucleus: new genes for old

Author: Jeremy N. Timmis, Michael Ayliffe, and Mathieu Rousseau-Gueutin
Subjects: Chloroplasts, DNA, Plant, Plant Science, Genes, Plant, Genome, Polymerase Chain Reaction, law.invention, Evolution, Molecular, chemistry.chemical_compound, law, Tobacco, medicine, Plastids, Plastid, Symbiosis, Gene, Polymerase chain reaction, Genetics, Cell Nucleus, Organelles, biology, food and beverages, biology.organism_classification, Article Addendum, Cell nucleus, medicine.anatomical_structure, chemistry, Eukaryote, Numt, DNA, Genome, Plant
Abstract: Nuclear genomes of eukaryotes are bombarded by a continuous deluge of organellar DNA which contributes significantly to eukaryote evolution. Here, we present a new PCR-based method that allows the specific amplification of nuclear integrants of organellar DNA (norgs) by exploiting recent deletions present in organellar genome sequences. We have used this method to amplify nuclear integrants of plastid DNA (nupts) from the nuclear genomes of several nicotiana species and to study the evolutionary forces acting upon these sequences. The role of nupts in endosymbiotic evolution and the different genetic factors influencing the time available for a chloroplastic gene to be functionally relocated in the nucleus are discussed.
Published: 2012

46. Promiscuous Organellar DNA

Author: Jeremy N. Timmis, Michael Ayliffe, Anna E. Sheppard, Mathieu Rousseau-Gueutin, Andrew H. Lloyd, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Adelaide, Data61 [Canberra] (CSIRO), Australian National University (ANU)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), R. Bock, and V. Knoop
Subjects: 0106 biological sciences, Mitochondrial DNA, Nuclear gene, [SDV]Life Sciences [q-bio], 01 natural sciences, Genome, 03 medical and health sciences, chemistry.chemical_compound, Chloroplast Genome, Organelle, Gene, Mitochondrial Genome, 030304 developmental biology, 0303 health sciences, Cytoplasmic Organelle, biology, food and beverages, biology.organism_classification, Cell biology, Nuclear Genome, Chloroplast DNA, chemistry, Eukaryote, DNA, 010606 plant biology & botany, Chloroplast Gene
Abstract: International audience; Endosymbiotic transfer of DNA from the cytoplasmic organelles (mitochondria and chloroplasts) to the nucleus has been a major factor driving the origin of new nuclear genes, a process central to eukaryote evolution. Typically, transfer of organelle DNA to the nucleus is quickly followed by decay, deletion and rearrangement. However, in rare instances these new sequences lead to functional relocation of organelle genes to the nucleus or the generation of genes with novel function. Similar transfer of chloroplast DNA has also added to the complexity of plant mitochondrial genomes. Significantly, these processes are ongoing, making promiscuous organellar DNA an important contributor to the continued evolution of plant genomes.
Published: 2012
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47. Conservation of Plastid Sequences in the Plant Nuclear Genome for Millions of Years Facilitates Endosymbiotic Evolution

Author: Jeremy N. Timmis, Michael Ayliffe, Mathieu Rousseau-Gueutin, University of Adelaide, Data61 [Canberra] (CSIRO), and Australian National University (ANU)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)
Subjects: 0106 biological sciences, Chloroplasts, Time Factors, Nuclear gene, DNA, Plant, Physiology, Molecular Sequence Data, Sequence alignment, Plant Science, Biology, Genes, Plant, medicine.disease_cause, Polymerase Chain Reaction, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, Tobacco, Genetics, Genomics, and Molecular Evolution, Genetics, medicine, Plastids, Plastid, Genome, Chloroplast, Symbiosis, Gene, Phylogeny, DNA Primers, 030304 developmental biology, Cell Nucleus, 0303 health sciences, Mutation, Base Sequence, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], DNA, Chloroplast, Sequence Analysis, DNA, chemistry, Evolutionary biology, Sequence Alignment, Genome, Plant, DNA, 010606 plant biology & botany
Abstract: The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed.
Published: 2011
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48. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes

Author: Mathieu Rousseau-Gueutin, Malika L. Aïnouche, K. Olbricht, Beatrice Denoyes-Rothan, Amèlia Gaston, G. Staudt, Abdelkader Aïnouche, L. Richard, INRA : UR419, Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Federal Research Centre for Cultivated Plants (JKI), Federal Research Centre for Cultivated Plants, Région Aquitaine INRA CIREF -Création variétale Fraises Fruits rouges, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Station de recherches fruitières, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, MESH: Genome, Plant, MESH: Sequence Analysis, DNA, MESH: Amino Acid Sequence, DHAR, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, MESH: Genes, Plant, MESH: Fragaria, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Plant Proteins, Genetics, 0303 health sciences, Duplicated gene, Phylogenetic tree, MESH: Plant Proteins, Fragaria, Reticulate evolution, GBSSI, Ploidy, Oxidoreductases, Genome, Plant, MESH: Cell Nucleus, Nuclear gene, DNA, Plant, Sequence analysis, [SDE.MCG]Environmental Sciences/Global Changes, Molecular Sequence Data, MESH: Sequence Alignment, Low-copy nuclear genes, Biology, Genes, Plant, 010603 evolutionary biology, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Starch Synthase, Species Specificity, Polyploid, Phylogenetics, MESH: Polyploidy, MESH: Species Specificity, Amino Acid Sequence, MESH: Oxidoreductases, MESH: Diploidy, MESH: DNA, Plant, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Cell Nucleus, MESH: Molecular Sequence Data, Sequence Analysis, DNA, Diploidy, MESH: Starch Synthase, Sequence Alignment
Abstract: International audience; Phylogenetic utility of two nuclear genes (GBSSI-2 and DHAR) was explored in genus Fragaria in order to clarify phylogenetic relationships among taxa and to elucidate the origin of the polyploid species. Orthology of the amplified products was assessed by several methods. Our results strongly suggest the loss of one GBSSI duplicated copy (GBSSI-1) in the Fragariinae subtribe. Phylogenetic analyses provided new insights into the evolutionary history of Fragaria, such as evidence supporting the presence of three main diploid genomic pools in the genus and demonstrating the occurrence of independent events of polyploidisation. In addition, the data provide evidence supporting an allopolyploid origin of the hexaploid F. moschata, and the octoploids F. chiloensis, F. iturupensis and F. virginiana. Accordingly, a new pattern summarizing our present knowledge on the Fragaria evolutionary history is proposed. Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes.
Published: 2009
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49. Use of a reference octoploid map for detecting homoeologous QTLs potentially involved in viability in the cultivated strawberry

Author: N. Pedeprat, Beatrice Denoyes-Rothan, L. Barrot, E. Lerceteau-Köhler, Mathieu Rousseau-Gueutin, Amèlia Gaston, Aurélie Petit, P. Chartier, D. Roca, ProdInra, Migration, Unité de recherches Espèces Fruitières et Vigne (UREFV), Institut National de la Recherche Agronomique (INRA), and Création Variétale Fraises Fruits Rouges (Ciref)
Subjects: 0106 biological sciences, QTL, [SDV]Life Sciences [q-bio], Population, POLYPLOIDY, Horticulture, Quantitative trait locus, CARTOGRAPHIE GENETIQUE, 01 natural sciences, Gene mapping, Genetic linkage, Botany, FRAISIER, Rosoideae, education, Genetics, education.field_of_study, biology, fungi, food and beverages, 04 agricultural and veterinary sciences, Fragaria, biology.organism_classification, FRAGARIA, [SDV] Life Sciences [q-bio], 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Microsatellite, Ploidy, COMPARATIVE GENETIC MAPPING, 010606 plant biology & botany
Abstract: International audience; The construction of a reference map of the complex octoploid cultivated strawberry was optimized by comparative mapping between Fragaria showing different levels of ploidy. In addition, this approach is a powerful tool for improving the detection of QTLs, and for a better understanding of the organization of these QTLs. By identifying the homoeologous linkage groups in the complex octoploid cultivated strawberry, potential homoeologous QTLs in Fragaria can be detected. The comparative mapping was based on two populations belonging to two different levels of Fragaria. The linkage map of the complex octoploid cultivated strawberry (Fragaria × ananassa Duch., 2n=8x=56) was based on a segregating population of 213 individuals of a cross between ‘Capitola’ and ‘CF1116’, two genotypes with many contrasting traits. This genetic map was compared to the diploid one, obtained from an interspecific cross between F. vesca and F. bucharica (Sargent et al., 2006). Based on 56 SSR markers common to both diploid and octoploid genetic maps, almost all linkage groups of the genetic octoploid map were arranged into the seven homoeologous groups (HGs) expected for the genus Fragaria, which belongs to the tribe Rosoideae. For each trait, QTLs can potentially be detected on each linkage group belonging to the same HG. Results showed detection of homoeologous chromosomal regions potentially involved in viability of the plant.
Published: 2009

50. Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry

Author: Amparo Monfort, D. W. Simpson, Beatrice Denoyes-Rothan, G. Guérin, E. Lerceteau-Köhler, Pere Arús, Laure Barrot, Mathieu Rousseau-Gueutin, Daniel J. Sargent, European Commission, Région Nouvelle-Aquitaine, Unité de recherches Espèces Fruitières et Vigne (UREFV), Institut National de la Recherche Agronomique (INRA), Création Variétale Fraises Fruits Rouges (Ciref), East Malling Research, and Institute of Agrifood Research and Technology (IRTA)
Subjects: 0106 biological sciences, DNA, Plant, Genetic Linkage, Molecular Sequence Data, Biology, CARTOGRAPHIE GENETIQUE, Investigations, 01 natural sciences, Genome, Fragaria, Chromosomes, Plant, Polyploidy, 03 medical and health sciences, Gene mapping, Meiosis, Genetic linkage, Genetics, Reference map, FRAISIER, Crosses, Genetic, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, ESPÈCE OCTOPLOÏDE, Chromosome Mapping, ESPÈCE DIPLOÏDE, Diploidy, Close relationship, Ploidy, Genome, Plant, 010606 plant biology & botany, Microsatellite Repeats
Abstract: Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. ×ananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. ×ananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry., This work was supported by grants from the Région Aquitaine and the European Community (Fonds Européen de Développement Régional, FEDER funds).
Published: 2008
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