142 research outputs found
The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants
Introduction: Ribosomal DNA (rDNA) loci have been widely used for identification of
allopolyploids and hybrids, although few of these studies employed high-throughput
sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE)
pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for
hybridogenic origin of species. Data were obtained from more than 80 plant species,
including several well-defined allopolyploids and homoploid hybrids of different
evolutionary ages and from widely dispersed taxonomic groups.
Results: (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In
contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs
composed of two or more interconnected loops representing intergenic spacers (IGS). (ii)
There was a relationship between graph complexity and locus numbers. (iii) The
sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were
congruent with those experimentally determined. (iv) Three-genomic comparative cluster
analysis of reads from allopolyploids and progenitor diploids allowed identification of
homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and
Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA
repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally
complex graph structures.
Conclusion: We found that the cluster graph shapes and graph parameters (k-mer
coverage scores and connected component index) well-reflect the organization and
intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA
cluster graphs computed by the RE pipeline together with the cytogenetic analysis might
be a reliable approach for the determination of the hybrid or allopolyploid plant species
parentage and may also be useful for detecting historical introgression events
Epigenetic changes in the context of recent hybridization and allopolyploid speciation in Spartina.
communication invitéeInternational audienc
Contexte génomique de la naissance d'une espèce : Histoire de la spartine anglaise
communication invitéeInternational audienc
Genome dynamics and environment: role of transposable elements in adaptation and speciation in plants
Communication oral
Epigenetic changes in the context of recent hybridization and allopolyploid speciation in Spartina.
communication invitéeInternational audienc
Spéciation allopolyploïde et évolution du génome des spartines envahissant les marais salés
International audienc
Evolutionary impact of hybridisation and genome duplication in plants.
conférence invitéeInternational audienc
Hybridization and polyploidy: Lessons from the invasive allopolyploid Spartina anglica.
California State UniversityInternational audienc
Evolution du génome des spartines polyploïdes envahissant les marais salés : apport des données de séquençage en masse (Roche 454)
communication oral
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