Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution
Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution
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DOI：
10.1038/nbt.3208
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发表时间：
2015-05-01
影响因子：
46.9
通讯作者：
Yu, Shuxun
中科院分区：
文献类型：
--
作者：
Li, Fuguang;Fan, Guangyi;Yu, Shuxun
陆地棉因其复杂的异源四倍体(A(T)D(T))基因组而难以测序。在这里，我们使用181倍的成对末端序列，辅以5倍的BAC-to-BAC序列和一个高分辨率的遗传图谱来产生一个基因组草图。在我们的组装中，88.5%的2,173-Mb支架被锚定并定位于26条假染色体上，它们覆盖了89.6%的A(T)D(T)基因组的96.7%。将该基因组与已测序的二倍体亚洲棉(Gossypium arboreum，AA)和雷蒙迪棉(Gossypium raimondii，DD)基因组进行比较，发现该基因组具有保守的基因序列。重复序列占AtDt基因组的67.2%，来自D-t的转座元件(TES)似乎比来自A(T)的更活跃。在异源多倍化后，A(T)D(T)基因组大小发生了缩小。A或A(T)基因组可能经历了纤维性状的正向选择。纤维素合酶(CESA)和1-氨基环丙烷-1-羧酸氧化酶1和3(ACO1，3)不同调控机制的协同进化可能对提高陆地棉纤维产量具有重要意义。
Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (A(t)D(t)) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%similar to 96.7% of the A(t)D(t) genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this Gossypium hirsutum A(t)D(t) genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from D-t seem more active than from A(t). Reduction in the A(t)D(t) genome size occurred after allopolyploidization. The A or A(t) genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in Gossypium hirsutum.