Li Qian, Zhang Yue, Zhang Zhengsheng, Li Xianbi, Yao Dan, Wang Yi, Ouyang Xufen, Li Yaohua, Song Wu, Xiao Yuehua
Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China.
College of Agronomy and Biological Science and Technology, Southwest University, Beibei, Chongqing, China.
Mol Genet Genomics. 2018 Feb;293(1):33-43. doi: 10.1007/s00438-017-1359-4. Epub 2017 Aug 28.
Retrotransposons comprise of a major fraction of higher plant genomes, and their proliferation and elimination have profound effects on genome evolution and gene functions as well. Previously we found a D-genome-originated Ty1/Copia-type LTR (DOCL) retrotransposon in the chromosome A08 of upland cotton. To further characterize the DOCL retrotransposon family, a total of 342 DOCL retrotransposons were identified in the sequenced cotton genomes, including 73, 157, and 112 from Gossypium raimondii, G. hirsutum, and G. barbadense, respectively. According to phylogenetic analysis, the DOCL family was divided into nine groups (G1-G9), among which five groups (G1-G4 and G9, including 292 members) were proliferated after the formation of tetraploid cottons. It was found that the majority of DOCL retrotransposons (especially those in G2, G3 and G9) inserted in non-allelic loci in G. hirsutum and G. barbadense, suggesting that their proliferations were relatively independent in different tetraploid cottons. Furthermore, DOCL retrotransposons inserted in coding regions largely eliminated expression of the targeted genes in G. hirsutum or G. barbadense. Our data suggested that recent proliferation of retrotransposon families like DOCL was one of important evolutionary forces driving diversification and evolution of tetraploid cottons.
逆转座子占高等植物基因组的很大一部分，它们的增殖和消除对基因组进化以及基因功能也有深远影响。此前我们在陆地棉的A08染色体上发现了一个源自D基因组的Ty1/Copia型长末端重复序列（DOCL）逆转座子。为了进一步表征DOCL逆转座子家族，在已测序的棉花基因组中总共鉴定出342个DOCL逆转座子，其中分别来自雷蒙德氏棉、陆地棉和海岛棉的有73个、157个和112个。根据系统发育分析，DOCL家族被分为九个组（G1-G9），其中五个组（G1-G4和G9，包括292个成员）是在四倍体棉花形成后增殖的。研究发现，大多数DOCL逆转座子（尤其是G2、G3和G9中的那些）插入到陆地棉和海岛棉的非等位基因位点，这表明它们在不同的四倍体棉花中的增殖相对独立。此外，插入编码区的DOCL逆转座子在很大程度上消除了陆地棉或海岛棉中靶向基因的表达。我们的数据表明，像DOCL这样的逆转座子家族的近期增殖是推动四倍体棉花多样化和进化的重要进化力量之一。
