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Homoeologous nonreciprocal recombination in polyploid cotton.
Salmon A, Flagel L, Ying B, Udall JA, Wendel JF. Salmon A, et al. New Phytol. 2010 Apr;186(1):123-34. doi: 10.1111/j.1469-8137.2009.03093.x. Epub 2009 Nov 19. New Phytol. 2010. PMID: 19925554
Here, we used genomic resources in diploid and allopolyploid cotton (Gossypium) to detect homoeologous single nucleotide polymorphisms provided by expressed sequence tags from G. arboreum (A genome), G. raimondii (D genome) and G. hirsutum (AD genome), allowing us to ident …
Here, we used genomic resources in diploid and allopolyploid cotton (Gossypium) to detect homoeologous single nucleotide polymorphisms provi …
Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina.
Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M. Parisod C, et al. New Phytol. 2009 Dec;184(4):1003-15. doi: 10.1111/j.1469-8137.2009.03029.x. Epub 2009 Sep 23. New Phytol. 2009. PMID: 19780987
*While no transposition burst was detected, we found evidence of major structural and CpG methylation changes in the vicinity of TE insertions accompanying hybridization, and to a lesser extent, genome doubling. ...Since most of this reorganization is conserved after genom …
*While no transposition burst was detected, we found evidence of major structural and CpG methylation changes in the vicinity of TE insertio …
Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae).
Rousseau H, Rousseau-Gueutin M, Dauvergne X, Boutte J, Simon G, Marnet N, Bouchereau A, Guiheneuf S, Bazureau JP, Morice J, Ravanel S, Cabello-Hurtado F, Ainouche A, Salmon A, Wendel JF, Ainouche ML. Rousseau H, et al. Mol Phylogenet Evol. 2017 Sep;114:401-414. doi: 10.1016/j.ympev.2017.07.003. Epub 2017 Jul 8. Mol Phylogenet Evol. 2017. PMID: 28694102
Thus, examination of DMSP synthesis in a phylogenetic context implicated a single origin of this physiological innovation, which occurred in the ancestor of the hexaploid Spartina lineage, 3-6MYA. Candidate genes specific to the Spartina DMSP biosynthesis pathway we …
Thus, examination of DMSP synthesis in a phylogenetic context implicated a single origin of this physiological innovation, whi …
The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco.
Gong L, Salmon A, Yoo MJ, Grupp KK, Wang Z, Paterson AH, Wendel JF. Gong L, et al. Mol Biol Evol. 2012 Oct;29(10):3023-36. doi: 10.1093/molbev/mss110. Epub 2012 Apr 3. Mol Biol Evol. 2012. PMID: 22490824
SSU copies from divergent (5-10 My) progenitor diploids ("A" and "D" genomes) were combined at the time of polyploid formation 1-2 Ma, with the LSU encoded by the maternal A-genome parent. ...Sequence data for the rbcS gene family revealed nonreciprocal homoeologous …
SSU copies from divergent (5-10 My) progenitor diploids ("A" and "D" genomes) were combined at the time of polyploid formation 1-2 Ma …
Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton.
Salmon A, Udall JA, Jeddeloh JA, Wendel J. Salmon A, et al. G3 (Bethesda). 2012 Aug;2(8):921-30. doi: 10.1534/g3.112.003392. Epub 2012 Aug 1. G3 (Bethesda). 2012. PMID: 22908041 Free PMC article.
A significant amount of flanking, nontargeted sequence (untranslated regions and introns) was also captured and sequenced along with the targeted exons. ...In addition, levels of heterozygosity appeared asymmetrical with respect to genome (A(T) or D(T)) in cultivate
A significant amount of flanking, nontargeted sequence (untranslated regions and introns) was also captured and sequenced along with
Targeted sequence capture as a powerful tool for evolutionary analysis.
Grover CE, Salmon A, Wendel JF. Grover CE, et al. Am J Bot. 2012 Feb;99(2):312-9. doi: 10.3732/ajb.1100323. Epub 2012 Jan 19. Am J Bot. 2012. PMID: 22268225
This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. ...Here we provide a brie …
This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, …
Polyploidy and DNA methylation: new tools available.
Salmon A, Ainouche ML. Salmon A, et al. Mol Ecol. 2010 Jan;19(2):213-5. doi: 10.1111/j.1365-294X.2009.04461.x. Mol Ecol. 2010. PMID: 20078770
New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangements and gene expression changes of different magnitudes depending on the different polyploid species investigated. ...As a result of s …
New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangemen …
Increased tolerance to organic xenobiotics following recent allopolyploidy in Spartina (Poaceae).
Cavé-Radet A, Salmon A, Lima O, Ainouche ML, El Amrani A. Cavé-Radet A, et al. Plant Sci. 2019 Mar;280:143-154. doi: 10.1016/j.plantsci.2018.11.005. Epub 2018 Nov 13. Plant Sci. 2019. PMID: 30823992
Genome doubling or polyploidy is a widespread phenomenon in plants where it has important evolutionary consequences affecting the species distribution and ecology. ...The neo-allopolyploid S. anglica appears as a potential candidate for phytoremediation in PAH-pollu …
Genome doubling or polyploidy is a widespread phenomenon in plants where it has important evolutionary consequences affecting the spe …
Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima.
Boutte J, Aliaga B, Lima O, Ferreira de Carvalho J, Ainouche A, Macas J, Rousseau-Gueutin M, Coriton O, Ainouche M, Salmon A. Boutte J, et al. G3 (Bethesda). 2015 Nov 3;6(1):29-40. doi: 10.1534/g3.115.023242. G3 (Bethesda). 2015. PMID: 26530424 Free PMC article.
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 hexaploi …
Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents …
The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating.
Rousseau-Gueutin M, Bellot S, Martin GE, Boutte J, Chelaifa H, Lima O, Michon-Coudouel S, Naquin D, Salmon A, Ainouche K, Ainouche M. Rousseau-Gueutin M, et al. Mol Phylogenet Evol. 2015 Dec;93:5-16. doi: 10.1016/j.ympev.2015.06.013. Epub 2015 Jul 13. Mol Phylogenet Evol. 2015. PMID: 26182838
In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using haploid markers like chloroplast genome sequences. ...Until now, only a few plastid markers were available to explore the history of th …
In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using ha …
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