Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Tianzhen ZhangYan HuWenkai JiangLei FangXueying GuanJie-Dan ChenJinbo ZhangChristopher A SaskiBrian E SchefflerDavid M StellyAmanda M Hulse-KempQun WanBingliang LiuChunxiao LiuSen WangMengqiao PanYangkun WangDawei WangWenxue YeLijing ChangWenpan ZhangQingxin SongRyan C KirkbrideXiaoya ChenElizabeth DennisDanny J LlewellynDaniel G PetersonPeggy ThaxtonDon C JonesQiong WangXiaoyang XuHua ZhangHuaitong WuLei ZhouGaofu MeiShuqi ChenYue TianDan XiangXinghe LiJian DingQiyang ZuoLinna TaoYunchao LiuJi LiYu LinYuanyuan HuiZhisheng CaoCaiping CaiXiefei ZhuZhi JiangBaoliang ZhouWangzhen GuoRuiqiang LiZ Jeffrey ChenPublished in: Nature biotechnology (2015)
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.