ArticleBMC genomics2012
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 106 citations in OpenAlex.
- CSSL-based GWAS identifies SNPs and candidate genes associated with Verticillium wilt resistance in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Two duplicated GhMML3 genes coordinately control development of lint and fuzz fibers in cotton.Plant communications · 2025Article
- Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica-indica subspecies.Nature plants · 2025Article
- Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton.Plant communications · 2024Article
- Review
- Applications of Virus-Induced Gene Silencing in Cotton.Plants (Basel, Switzerland) · 2024Review
- Genome-Wide Identification and Functional Analysis ofPlants (Basel, Switzerland) · 2023Article
- Article
- Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes.Molecular biology and evolution · 2022Article
- Subgenome evolution in allotetraploid plants.The Plant journal : for cell and molecular biology · 2021Article
- Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.Briefings in bioinformatics · 2021Review
- A major quantitative trait locus on chromosome A9, BnaPh1, controls homoeologous recombination in Brassica napus.The New phytologist · 2021Article
- Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses.BMC genomics · 2020Article
- Extensive changes in gene expression and alternative splicing due to homoeologous exchange in rice segmental allopolyploids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica.Scientific reports · 2019Article
- Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton.International journal of molecular sciences · 2019Article
- Article
- A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids.Genetics · 2018Article
- Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation.The New phytologist · 2018Article
- Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing.Genome biology and evolution · 2017Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundModern allotetraploid cotton contains an "A" and "D" genome from an ancestral polyploidy event that occurred approximately 1-2 million years ago. Diploid A- and D-genome species can be compared to the A- and D-genomes found within these allotetraploids to make evolutionary inferences about polyploidy. In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data.
resultsWe generated a set of cotton expressed sequence tags (ESTs), comprising approximately 4.4 million Sanger and next-generation (454) transcripts supplemented by approximately 152 million Illumina reads from diploid and allotetraploid cottons. From the EST alignments we inferred 259,192 genome-specific single nucleotide polymorphisms (SNPs). Molecular evolutionary analyses of protein-coding regions demonstrate that the rate of nucleotide substitution has increased among both allotetraploid genomes relative to the diploids, and that the ratio of nonsynonymous to synonymous substitutions has increased in one of the two polyploid lineages we sampled. We also use these SNPs to show that a surprisingly high percentage of duplicate genes (~7 %) show a signature of non-independent evolution in the allotetraploid nucleus, having experienced one or more episodes of nonreciprocal homoeologous recombination (NRHR).
conclusionsIn this study we characterize the functional and mutational properties of the cotton transcriptome, produce a large genome-specific SNP database, and detect illegitimate genetic exchanges between duplicate genomes sharing a common allotetraploid nucleus. Our findings have important implications for our understanding of the consequences of polyploidy and duplicate gene evolution. We demonstrate that cotton genes have experienced an increased rate of molecular evolution following duplication by polyploidy, and that polyploidy has enabled considerable levels of nonreciprocal exchange between homoeologous genes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.