ArticleG3 (Bethesda, Md.)2013
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 88 citations in OpenAlex.
- The polyploid continuum and the landscape of polyploid genomic variation.American journal of botany · 2025Review
- Green synthesized silver nanoparticles enhance drought tolerance in cotton plants cultured in vitro.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz.Scientific reports · 2023Article
- Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids.Genome biology and evolution · 2022Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research.Plants (Basel, Switzerland) · 2021Article
- Changes in secondary metabolites and fiber quality of cotton (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum.BMC genomics · 2020Article
- Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution.Frontiers in plant science · 2019Article
- SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population.Molecular genetics and genomics : MGG · 2018Article
- The cotton MAPK kinase GhMPK20 negatively regulates resistance to Fusarium oxysporum by mediating the MKK4-MPK20-WRKY40 cascade.Molecular plant pathology · 2018Article
- Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress.BMC plant biology · 2018Article
- Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).Molecular genetics and genomics : MGG · 2017Article
- Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq.BMC genomics · 2017Article
- Lipid metabolites in seeds of diverse Gossypium accessions: molecular identification of a high oleic mutant allele.Planta · 2017Article
- Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.).3 Biotech · 2016Review
- Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).Genome biology and evolution · 2016Article
- Mapping of fiber quality QTLs reveals useful variation and footprints of cotton domestication using introgression lines.Scientific reports · 2016Article
- Independent Domestication of Two Old World Cotton Species.Genome biology and evolution · 2016Article
- DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.PLoS genetics · 2016Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.
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