ArticleScientific reports2017
Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- The evolution of gene expression in allopolyploid cotton relative to parental diploids and induced haploids.aBIOTECH · 2026Article
- Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton.Genes · 2024Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes.Molecular biology and evolution · 2022Article
- Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Genomic Characterization of the Fruity Aroma Gene,Frontiers in plant science · 2021Article
- Article
- Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.Nature genetics · 2020Article
- Genetic Analysis of the Transition from Wild to Domesticated Cotton (G3 (Bethesda, Md.) · 2020Article
- Unraveling cis and trans regulatory evolution during cotton domestication.Nature communications · 2019Article
- Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution.Genes · 2019Article
- Identification of cotton MOTHER OF FT AND TFL1 homologs, GhMFT1 and GhMFT2, involved in seed germination.PloS one · 2019Article
- Cotton CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING genes functionally diverged to differentially impact plant architecture.Journal of experimental botany · 2018Article
- Abundant Small Genetic Alterations after Upland Cotton Domestication.BioMed research international · 2018Article
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13 authors.
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Abstract
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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