Unequal Accumulation Of Nucleotide Diversity In The Two Co-Resident Genomes Of Allopolyploid Cotton

Autor: Szadkowski, Emmanuel, Page, Justin T., Udall, Josh A., Jeddeloh, J.A., Grover, Corrinne E., Grupp, Kara K., Salmon, Armel, Wendel, Jonathan F.
Přispěvatelé: Department of Botany, National University of Ireland [Galway] (NUI Galway), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Roche Nimblegen Inc., 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), ProdInra, Archive Ouverte, 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)
Jazyk: angličtina
Rok vydání: 2013
Předmět:
Zdroj: Plant and Animal Genomes Conference
Plant and Animal Genomes Conference, Jan 2013, San Diego, United States
Popis: Rates of molecular evolution are highly variable within and among genes and among lineages. The forces responsible for this variation include a suite of internal genomic mechanisms (e.g., recombinational environment, repair efficiency) and external population level phenomena (e.g., selection, effective population size). A promising model for disentangling intrinsic and extrinsic forces are allopolyploid plants, which combine two (or more) set of homoeologous genes in a single nucleus and in the same ecological context. Thus, the null hypothesis may be tested that homoeologs will accumulate nucleotide diversity at equivalent rates in a set of populations within a species. Here we test this hypothesis using Gossypium hirsutum (cotton), a natural allopolyploid derived from the merger, 1-2 million years ago (MYA) of progenitor diploid genomes (A and D), which diverged from a common ancestor ~5-10 million years ago. Homoeologous chromosomes in the allopolyploid (AT and DtT remain highly similar to those of their diploid orthologs, with high synteny and colinearity. Using sequence capture and 454 sequencing, we screened 40 diverse G. hirsutum accessions, targeting exonic regions in ~400 homoeologous gene pairs. Analyzed sequences included approximately twice the target space, due to recovery of introns and flanking UTRs. Nucleotide diversity levels in G. hirsutum are low, consistent with earlier indications. Notwithstanding this low level of overall diversity, preliminary analyses suggest that diversity is higher in the At genome than the Dt genome, genome-wide. This enhanced diversity may reflect differences related to the two-fold difference in progenitor genome size. Our results demonstrate that genic environment plays a key role in the genesis of genetic novelty, and how allopolyploidy can create novel allelic combinations with the potential for adaptive traits.
Databáze: OpenAIRE
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