Genome

Gossypium hirsutum (cotton) cultivated tetraploid cotton Lineage: Eukaryota[15558]; Viridiplantae[1758]; Streptophyta[1641]; Embryophyta[1630]; Tracheophyta[1603]; Spermatophyta[1585]; Magnoliopsida[1558]; eudicotyledons[1256]; Gunneridae[1256]; Pentapetalae[1256]; rosids[782]; malvids[313]; Malvales[54]; Malvaceae[49]; Malvoideae[37]; Gossypium[29]; Gossypium hirsutum[1]

The genus Gossypium comprises of several different cotton species. It is a major agronomic fiber crop and an important oilseed that is native to the tropics and the warm temperate regions. Cotton seeds produce trichomes, specialized seed hairs, which are among the longest plant cells. Apart from its economic importance, cotton is also biologically More...significant and makes an interesting system to study fundamental cellular processes related to cell differentiation, cell expansion, and cell wall modifications.Cultivated cotton exists in both diploid ( 2n = 26) as well as allotetraploid (2n = 4x = 52) varieties. Diploid cotton fall into eight different genome types designated A to G and K. Most significant commercial variety in US is tetraploid cotton, G. hirsutum. It is the combination of A and D genomes to form AD genome. G. hirsutum is a commercially important cotton variety grown in many parts of the world. It is an allotetraploid with 2n = 52 chromosomes. International Cotton Genome Initiative has been established to facilitate global cotton research by increasing knowledge and resource integration and coordinated research planning.Clemson University Genomics Institute has constructed a BAC library from G. hirsutum which can be used for physical mapping and cloning of genes of agronomical importance. Less...

Summary Sequence data:  genome assemblies: 13; sequence reads: 24  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 2305.1  median protein count: 169081  median GC%: 34.4232 NCBI Annotation Release:  101 Publications (limited to 20 most recent records) Genomic and epigenomic insights into the mechanism of cold response in upland cotton (Gossypium hirsutum). Wang J, et al. Plant Physiol Biochem 2024 Jan Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.). Perkin LC, et al. G3 (Bethesda) 2021 Oct 19 Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Chen ZJ, et al. Nat Genet 2020 May Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Yang Z, et al. Nat Commun 2019 Jul 5 Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Li F, et al. Nat Biotechnol 2015 May The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. Lee SB, et al. BMC Genomics 2006 Mar 23 More...  Representative (genome information for reference and representative genomes) Reference genome:   Gossypium hirsutum Gossypium_hirsutum_v2.1 Submitter: HudsonAlpha Genome Sequencing Center Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr A01 NC_053424.1 CM017662.1 119.76 35.0 3,677 1 39 1,895 3,808 243 Chr A02 NC_053425.1 CM017663.1 108.14 35.1 3,104 1 24 1,511 3,023 176 Chr A03 NC_053426.1 CM017664.1 113.69 34.9 3,778 - 44 1,688 3,530 218 Chr A04 NC_053427.1 CM017665.1 89.18 35.1 2,562 - 78 1,200 2,710 185 Chr A05 NC_053428.1 CM017666.1 111.1 34.3 6,754 13 86 2,068 5,538 394 Chr A06 NC_053429.1 CM017667.1 128.2 35.0 3,834 1 52 1,981 3,691 207 Chr A07 NC_053430.1 CM017668.1 98.9 34.7 3,843 52 46 2,016 3,826 233 Chr A08 NC_053431.1 CM017669.1 127.5 35.0 4,321 7 37 1,993 4,212 271 Chr A09 NC_053432.1 CM017670.1 85.34 34.6 4,177 219 73 1,341 3,893 297 Chr A10 NC_053433.1 CM017671.1 118.18 34.7 4,238 - 72 1,763 3,952 235 Chr A11 NC_053434.1 CM017672.1 124.18 34.7 5,736 16 77 1,840 5,096 356 Chr A12 NC_053435.1 CM017673.1 109.47 34.8 4,564 5 43 1,737 4,122 288 Chr A13 NC_053436.1 CM017674.1 111.65 34.8 4,147 - 70 1,895 3,917 257 Chr D01 NC_053437.1 CM017675.1 65.21 33.6 3,782 - 43 1,426 3,280 209 Chr D02 NC_053438.1 CM017676.1 72.19 33.6 4,048 - 36 1,299 3,486 227 Chr D03 NC_053439.1 CM017677.1 54.96 33.6 2,999 2 45 1,056 2,551 163 Chr D04 NC_053440.1 CM017678.1 58.23 33.6 3,360 - 55 1,243 2,834 184 Chr D05 NC_053441.1 CM017679.1 66.48 33.4 6,632 - 82 1,400 4,896 328 Chr D06 NC_053442.1 CM017680.1 66.68 33.5 3,831 13 49 1,427 3,177 189 Chr D07 NC_053443.1 CM017681.1 59.44 33.4 3,910 - 42 1,437 3,210 167 Chr D08 NC_053444.1 CM017682.1 69.43 33.6 4,548 9 41 1,552 3,591 216 Chr D09 NC_053445.1 CM017683.1 54.45 33.3 4,191 267 60 1,137 3,887 585 Chr D10 NC_053446.1 CM017684.1 68.09 33.4 4,464 - 72 1,566 3,697 197 Chr D11 NC_053447.1 CM017685.1 72.82 33.4 5,936 1 62 1,536 4,648 304 Chr D12 NC_053448.1 CM017686.1 63.26 33.6 4,706 4 49 1,347 3,645 223 Chr D13 NC_053449.1 CM017687.1 65.1 33.6 4,135 - 63 1,321 3,420 235 MT NC_027406.1 - 0.67 45.0 34 4 29 - 68 1 Pltd NC_007944.1 - 0.16 37.2 83 8 37 - 129 1 Un - . - 23.62 37.3 450 747 42 317 1,619 364 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources ARS CottonDB Cirad