State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
BGI-Shenzhen, Shenzhen, China.
Nat Biotechnol. 2015 May;33(5):524-30. doi: 10.1038/nbt.3208. Epub 2015 Apr 20.
Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) 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%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt 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 Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At 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 G. hirsutum.
由于其复杂的异源四倍体（AtDt）基因组，陆地棉的测序一直很困难。在这里，我们使用 181 倍的配对末端序列，结合五倍的 BAC 到 BAC 序列和高分辨率遗传图谱，生成了一个草图基因组。在我们的组装中，2173-Mb 支架中有 88.5%被锚定并定向到 26 个假染色体上，这些支架覆盖了 AtDt 基因组的 89.6%∼96.7%。将这个陆地棉 AtDt 基因组与已经测序的二倍体陆地棉（AA）和海岛棉（DD）基因组进行比较，发现了保守的基因顺序。重复序列占 AtDt 基因组的 67.2%，来自 Dt 的转座元件（TEs）似乎比来自 At 的更活跃。异源四倍化后，AtDt 基因组的大小发生了减少。A 或 At 基因组可能经历了纤维性状的正选择。不同调控机制的协同进化对纤维素合酶（CesA）和 1-氨基环丙烷-1-羧酸氧化酶 1 和 3（ACO1,3）的协同进化可能对提高陆地棉的纤维产量很重要。
