Unequal accumulation of nucleotide diversity in the two co-resident genomes of allopolyploid cotton The correlation of DNA methylation and homoeologous gene expression in cotton pearl

International audienc

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

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

Unequal accumulation of nucleotide diversity in the two co-resident genomes of allopolyploid cotton The correlation of DNA methylation and homoeologous gene expression in cotton pearl

International audienc

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

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

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement