Insights into the Evolution of the Ne World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing
Insights into the Evolution of the Ne World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing
复制标题
DOI：
10.1093/gbe/evy256
复制
发表时间：
2019-01-01
影响因子：
3.3
通讯作者：
Wendel, Jonathan F.
中科院分区：
文献类型：
--
作者：
Grover, Corrinne E.;Arick, Mark A., II;Wendel, Jonathan F.
本研究采用染色体组学方法研究了分布广泛的新世界二倍体棉（Gossypium，subg. Houzingenia）。全基因组重测序数据（平均33 ×基因组覆盖率）的产生，重新评估亚属的系统发育史，并提供一个时间框架，其多样化。系统发育分析表明，该亚属可能起源于6.6马从非洲的跨洋传播，但几乎所有的生物多样性进化后，在更新世中期（0.5-2.0马）的快速多样化，与多个长距离的传播需要考虑到亚利桑那州，加拉帕戈斯群岛，和秘鲁的范围扩展。cpDNAversus核数据的比较分析表明，这一历史是伴随着几个明确的情况下种间渐渗。重复DNA占总880 Mb基因组的大约一半，但大多数转座因子家族相对古老且在物种中稳定。在基因部分，成对的同义突变率平均每百万年1%，与非同义的变化是约7倍的频率。检测到超过110万个indel，并在遗传学上极化，揭示了2倍于小插入的缺失偏倚。我们认为，这种基因组缩小的偏见抵消TE扩增和插入基因组大小的增长，并有助于解释相对较小的基因组，仅限于这个亚属。与核苷酸替换率相比，indel发生率低得多，平均每个indel事件约17个核苷酸替换。
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33 x genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.