Spéciation allopolyploïde et dynamique fonctionnelle du génome chez les Spartines

evolution following divergent and reticulate speciation at the polyploid level was examined in species from the genus Spartina (Poaceae) that play an important role in the salt marsh sedimentary dynamics. Transcriptomic changes were analysed using restriction polymorphisms and microarrays. Divergent speciation was examined between the two sister hexaploid species, the declining S. maritima from Western Europe and the invasive S. alterniflora. In spite of limited nucleotide divergence, these species exhibit consistent expression differences. The consequences of interspecific hybridisation and genome duplication were analysed in two recently and independently formed F1 hybrids (S. x neyrautii & S. x townsendii) sharing the same parents and in the invasive allopolyploid S. anglica. The results indicate significant, though different effects of hybridisation and genome duplication on the transcriptome, with maternal expression dominance in the F1 hybrids, that is attenuated in the allopolyploid which is characterized by overexpressed genes. Sequences flanking Ins2, Wis-like, Cassandra transposable elements seem to be affected by a similar dynamics. The two independent hybridisation events had different transcriptomic effects, in agreement with their different morphologies. The functional categories of the differentially expressed genes are discussed in the context of the phenotypic and ecological differences between the analysed species.La spéciation est un mécanisme central de la diversification biologique. Ce travail vise à analyser l'évolution transcriptomique accompagnant la spéciation chez les spartines (Poaceae) qui jouent un rôle important dans la dynamique sédimentaire des marais salés. Ce genre est caractérisé par différents types de spéciation divergente et réticulée au niveau polyploïde. L'évolution du transcriptome par différentes analyses de polymorphisme et par microarrays a été analysée chez deux espèces soeurs hexaploïdes S. maritima (en régression en Europe) et S. alterniflora (envahissante). Malgré une faible divergence nucléotidique, ces deux espèces montrent des différences d'expression importantes. Les conséquences de l'hybridation et de la duplication du génome ont été examinées chez deux hybrides F1 (S. x neyrautii et S. x townsendii) formés récemment et indépendamment à partir des mêmes parents, et chez l'allopolyploïde envahissant S. anglica. Nos résultats ont montré les effets importants, mais différents de l'hybridation et de la duplication du génome sur le transcriptome. Cet effet se manifeste par une dominance d'expression maternelle (chez les hybrides F1) qui s'atténue chez l'allopolyploïde. Ce dernier se distingue par une surexpression de la majorité des gènes. Les régions flanquant les éléments transposables Ins2, Wis-like, Cassandra apparaissent également affectées par cette dynamique. Les deux événements d'hybridation ont engendré des réponses différentes, en accord avec la morphologie très différente des hybrides. Les catégories de gènes différentiellement exprimées entre les espèces sont discutées dans le contexte des différences phénotypiques et écologiques de ces espèces

Spéciation allopolyploïde et dynamique fonctionnelle du génome chez les Spartines

evolution following divergent and reticulate speciation at the polyploid level was examined in species from the genus Spartina (Poaceae) that play an important role in the salt marsh sedimentary dynamics. Transcriptomic changes were analysed using restriction polymorphisms and microarrays. Divergent speciation was examined between the two sister hexaploid species, the declining S. maritima from Western Europe and the invasive S. alterniflora. In spite of limited nucleotide divergence, these species exhibit consistent expression differences. The consequences of interspecific hybridisation and genome duplication were analysed in two recently and independently formed F1 hybrids (S. x neyrautii & S. x townsendii) sharing the same parents and in the invasive allopolyploid S. anglica. The results indicate significant, though different effects of hybridisation and genome duplication on the transcriptome, with maternal expression dominance in the F1 hybrids, that is attenuated in the allopolyploid which is characterized by overexpressed genes. Sequences flanking Ins2, Wis-like, Cassandra transposable elements seem to be affected by a similar dynamics. The two independent hybridisation events had different transcriptomic effects, in agreement with their different morphologies. The functional categories of the differentially expressed genes are discussed in the context of the phenotypic and ecological differences between the analysed species.La spéciation est un mécanisme central de la diversification biologique. Ce travail vise à analyser l'évolution transcriptomique accompagnant la spéciation chez les spartines (Poaceae) qui jouent un rôle important dans la dynamique sédimentaire des marais salés. Ce genre est caractérisé par différents types de spéciation divergente et réticulée au niveau polyploïde. L'évolution du transcriptome par différentes analyses de polymorphisme et par microarrays a été analysée chez deux espèces soeurs hexaploïdes S. maritima (en régression en Europe) et S. alterniflora (envahissante). Malgré une faible divergence nucléotidique, ces deux espèces montrent des différences d'expression importantes. Les conséquences de l'hybridation et de la duplication du génome ont été examinées chez deux hybrides F1 (S. x neyrautii et S. x townsendii) formés récemment et indépendamment à partir des mêmes parents, et chez l'allopolyploïde envahissant S. anglica. Nos résultats ont montré les effets importants, mais différents de l'hybridation et de la duplication du génome sur le transcriptome. Cet effet se manifeste par une dominance d'expression maternelle (chez les hybrides F1) qui s'atténue chez l'allopolyploïde. Ce dernier se distingue par une surexpression de la majorité des gènes. Les régions flanquant les éléments transposables Ins2, Wis-like, Cassandra apparaissent également affectées par cette dynamique. Les deux événements d'hybridation ont engendré des réponses différentes, en accord avec la morphologie très différente des hybrides. Les catégories de gènes différentiellement exprimées entre les espèces sont discutées dans le contexte des différences phénotypiques et écologiques de ces espèces

Spéciation allopolyploïde et dynamique fonctionnelle du génome chez les Spartines

La spéciation est un mécanisme central de la diversification biologique. Ce travail vise à analyser l évolution transcriptomique accompagnant la spéciation chez les spartines (Poaceae) qui jouent un rôle important dans la dynamique sédimentaire des marais salés. Ce genre est caractérisé par différents types de spéciation divergente et réticulée au niveau polyploïde. L évolution du transcriptome par différentes analyses de polymorphisme et par microarrays a été analysée chez deux espèces sœurs hexaploïdes S. maritima (en régression en Europe) et S. alterniflora (envahissante). Malgré une faible divergence nucléotidique, ces deux espèces montrent des différences d expression importantes. Les conséquences de l hybridation et de la duplication du génome ont été examinées chez deux hybrides F1 (S. x neyrautii et S. x townsendii) formés récemment et indépendamment à partir des mêmes parents, et chez l allopolyploïde envahissant S. anglica. Nos résultats ont montré les effets importants, mais différents de l hybridation et de la duplication du génome sur le transcriptome. Cet effet se manifeste par une dominance d expression maternelle (chez les hybrides F1) qui s atténue chez l allopolyploïde. Ce dernier se distingue par une sur-expression de la majorité des gènes. Les régions flanquant les éléments transposables Ins2, Wis-like, Cassandra apparaissent également affectées par cette dynamique. Les deux événements d hybridation ont engendré des réponses différentes, en accord avec la morphologie très différente des hybrides. Les catégories de gènes différentiellement exprimées entre les espèces sont discutées dans le contexte des différences phénotypiques et écologiques de ces espèces.Speciation is a central process to biological diversification. In this study, transcriptome evolution following divergent and reticulate speciation at the polyploid level was examined in species from the genus Spartina (Poaceae) that play an important role in the salt marsh sedimentary dynamics. Transcriptomic changes were analysed using restriction polymorphisms and microarrays. Divergent speciation was examined between the two sister hexaploid species, the declining S. maritima from Western Europe and the invasive S. alterniflora. In spite of limited nucleotide divergence, these species exhibit consistent expression differences. The consequences of interspecific hybridisation and genome duplication were analysed in two recently and independently formed F1 hybrids (S. x neyrautii & S. x townsendii) sharing the same parents and in the invasive allopolyploid S. anglica. The results indicate significant, though different effects of hybridisation and genome duplication on the transcriptome, with maternal expression dominance in the F1 hybrids, that is attenuated in the allopolyploid which is characterized by overexpressed genes. Sequences flanking Ins2, Wis-like, Cassandra transposable elements seem to be affected by a similar dynamics. The two independent hybridisation events had different transcriptomic effects, in agreement with their different morphologies. The functional categories of the differentially expressed genes are discussed in the context of the phenotypic and ecological differences between the analysed species.RENNES1-BU Sciences Philo (352382102) / SudocSudocFranceF

Reprogramming of gene expression in the genetically stable bread allohexaploid wheat

International audienceBrassica species have a long common history with polyploidy, and in the last two decades their study has contributed to renewed interest in plant polyploidy research. During this time they have served as fruitful models with which to further our understanding of questions relating to innovation, adaptation, and the evolutionary success of polyploids. Brassica species have undergone recurrent rounds of polyploidy, and therefore provide ways to analyze the consequences of polyploidy over different timescales. Studies on resynthesized Brassica allotetraploids (specifically on synthetic oilseed rape, B. napus) have highlighted the high structural plasticity of the newly formed allopolyploid genome as well as highlighting numerous expression changes, both of which drive rapid generation of phenotypic variation. Increasingly accumulating evidence has revealed the broad diversity of the mechanisms and levels of regulation (genetically or epigenetically controlled) at the origins of the high dynamics of the newly formed Brassica polyploid genome. In the very near future, the availability of the complete genome sequence of the natural B. napus together with genome sequences of its two diploid progenitors B. rapa and B. oleracea will certainly enable further understanding of the many mechanisms that have contributed to the evolution of the Brassica genome

Transcriptomic changes following recent natural hybridization and allopolyploid in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae)

International audience• Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaptation of newly formed allopolyploid species. In spite of the significant progress made in recent years, few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions.• We used Agilent rice oligomicroarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classic example of recent allopolyploid speciation: S. anglica formed during the 19th century following genome duplication of the hybrid S. · townsendii.• Our data indicate important, but different, effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance was attenuated following genome duplication in S. anglica, but this species exhibits an increased number of transgressively overexpressed genes.• These results reflect the decoupled effects of the ‘genomic shock’ following hybridization and genome redundancy on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploid

Transcriptomic changes following recent natural hybridization and allopolyploid in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae)

International audience• Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaptation of newly formed allopolyploid species. In spite of the significant progress made in recent years, few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions.• We used Agilent rice oligomicroarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classic example of recent allopolyploid speciation: S. anglica formed during the 19th century following genome duplication of the hybrid S. · townsendii.• Our data indicate important, but different, effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance was attenuated following genome duplication in S. anglica, but this species exhibits an increased number of transgressively overexpressed genes.• These results reflect the decoupled effects of the ‘genomic shock’ following hybridization and genome redundancy on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploid

Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae)

International audienceInvasive species are ideal model systems to investigate the evolutionary processes associated with their ecological success by comparison with closely related species. In this article, we explore transcriptome evolution following divergence between two closely related salt-marsh species, the invasive Spartina alterniflora (native to the East- American Atlantic coast, introduced in several continents) and the declining Spartina maritima (native to the Euro-African Atlantic coast). We have explored the utility of cross-species hybridization microarrays using rice (Oryza sativa) oligo-microarrays to compare leaf expression patterns between these species. Coding sequence comparisons from 10 nuclear genes (2256 bp) revealed that nucleotide divergence between Spartina and Oryza range from 8% to 14%. More than 70% of the 60-mer oligonucleotide sequences spotted on the rice microarray exhibited stable and repeatable patterns when hybridized against Spartina RNA. In total, 9353 (44.5%) genes on the array hybridized with both species S. maritima and S. alterniflora. Among these genes, 1247 genes were found to be differentially expressed between the two Spartina species, most of them (957) being up-regulated in S. alterniflora. In particular, developmental and cellular growth genes (gene ontology, biological process) were highly up-regulated in S. alterniflora and down-regulated in S. maritima, whereas genes involved in stress response were upregulated in S. maritima. Our findings indicate the suitability of cross-species microarray hybridization between Spartina and O. sativa and reveal the extent of leaf transcriptome evolution that took place during the divergence between S. alterniflora and S. maritima. Expression patterns are consistent with the morphological differentiation and differential expansion of the two species

Cross species hybridisation microarrays reeal consistent transcriptomic changes following natural interspecific hybridisation and allopolyploid speciation in Spartina (Poaceae).

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Ecological genomics of the recent Spartina hybrids and allopolyploid invading salt-marshes

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