Wang Jianhua, Han Guan-Zhu
Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
Mol Biol Evol. 2021 Jul 29;38(8):3267-3278. doi: 10.1093/molbev/msab101.
LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
长末端重复序列（LTR）逆转录转座子是真核生物基因组的主要组成部分。偶尔，逆转录转座子基因会被其宿主招募来执行多种功能，这一过程被正式称为共选项。然而，真核生物中LTR逆转录转座子gag基因共选项的全貌仍然缺乏，仅有几例记录在案的情况专门涉及动物中的Ty3/Gypsy逆转录转座子。在这里，我们使用系统发育基因组学方法，系统地发掘2011种真核生物在分类科级以上水平上逆转录转座子gag基因的共选项，即真核生物深度进化过程中发生的共选项。我们在超过740个真核生物家族中总共鉴定出14个独立的gag基因共选项事件，其中8个此前未被报道。在这些逆转录转座子gag基因共选项事件中，9个、4个和1个分别涉及Ty3/Gypsy、Ty1/Copia和Bel-Pao逆转录转座子的gag基因。7个、4个和3个共选项事件分别发生在动物、植物和真菌中。有趣的是，两个共选项事件发生在被子植物的早期进化过程中。选择性压力和基因表达分析都进一步支持这些被共选的gag基因可能在其宿主中执行多种细胞功能，并且几个被共选的gag基因可能受到正选择。综上所述，我们的结果提供了真核生物深度进化过程中发生的LTR逆转录转座子gag基因共选项事件的全貌，并表明真核生物深度进化过程中LTR逆转录转座子gag基因共选项较少。
