Anyang Institute of Technology, Anyang, Henan, 455000, China.
State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
Sci Rep. 2018 Jun 20;8(1):9399. doi: 10.1038/s41598-018-27589-6.
Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.
长末端重复（LTR）反转录转座子是最丰富的 DNA 成分，在很大程度上导致了植物基因组大小的变异。尽管在植物物种中已经进行了研究，但对于棉花这种最重要的纤维和质地作物，可用的数据非常有限。在这项研究中，我们对四个棉花物种中的 LTR 反转录转座子家族进行了全面分析。在四倍体棉属物种中，来自祖先 D 基因组的 LTR 反转录转座子家族在 D 亚基因组中有更多的拷贝，而来自祖先 A 基因组的家族在 A 亚基因组中有更多的拷贝。一些在多倍体形成后插入的 LTR 反转录转座子家族可能仍然将其大部分拷贝分布在一个亚基因组中。该数据还表明，10~200 个拷贝的家族是丰富的，它们对棉属基因组大小有很大的影响；相反，少数高拷贝 LTR 反转录转座子家族对基因组大小的贡献较小。Kimura 距离分布表明，高拷贝数家族不是近期爆发的，家族拷贝数与进化时期之间没有明显的关系。进一步的分析表明，每个 LTR 反转录转座子家族在棉花中可能都有其自身的分布特征。
