家蚕微孢子虫和柞蚕微孢子虫LINE类反转录转座子R4的鉴定及系统进化分析

Identification and Phylogenetic Analysis of LINE Retrotransposons R4 in Nosema bombycis and Nosema pernyi

反转录转座子在物种基因组的进化中发挥重要作用,LINE元件属于non-LTR反转录转座子的类型之一。通过生物信息学分析方法,鉴定了一个全长3 855 bp的柞蚕微孢子虫(Nosema pernyi)LINE元件R4Na和一个全长3 970 bp的家蚕微孢子虫(Nosema bombycis)LINE元件R4Nb。R4Na在柞蚕微孢子虫基因组中有4个呈串联排列的完整拷贝,其余拷贝序列结构和R4Nb的拷贝序列结构有很大差异,显示二者的变异程度很大,暗示2种微孢子虫比较古老。利用转录组高通量测序库比对,R4Nb反转录酶编码区插入的外源序列具有转录活性,暗示这段外源序列可能被招募为外显子。依据LINE元件的反转录酶结构域序列构建2种微孢子虫以及东方蜜蜂微孢子虫(Nosema ceranae)、西方蜜蜂微孢子虫(Nosema apis)、按蚊微孢子虫(Anncaliia algerae)的系统进化树,结果显示R4Na和R4Nb与其它昆虫微孢子虫的R4元件具有一定相似性,而且R4元件家族在昆虫微孢子虫基因组分化过程中形成明显的3个进化群。研究结果证明家蚕微孢子虫和柞蚕微孢子虫的基因组中均存在LINE类反转录转座子,为研究2种微孢子虫的基因组结构提供了新的线索。

Retrotransposons play important roles in genome evolution.LINE element is a kind of non-LTR retrotransposons.In this study,LINE elements R4 Na with full-length of 3 855 bp and R4 Nb with full-length of 3 970 bp were identified in Nosema pernyi and in Nosema bombycis respectively by bioinformatics analysis.A four tandem repeats of R4 Na was distributed in the N.pernyi genome,whereas other copies showed significant difference with that of R4 Nb,implying that these two microsporidian species should have diverged at ancient time.Alignment in database of transcriptomic high-throughput sequencing showed that the sequence inserted in the coding region of R4 Nb reverse transcriptase had transcriptional activity,which suggested that it was recruited as exon.Phylogenetic tree constructed using LINE reverse transcriptase sequences of these two microsporidian species with Nosema ceranae,Nosema apis,and Anncaliia algerae indicated that elements of R4 Na and R4 Nb shared high similarity with R4 elements of other microsporidian species.Moreover,R4 families from Nosema species can be divided into three evolutionary groups along with the genome differentiation of microsporidian in insects.Our results demonstrated that LINE retrotransposon existedin both Nosema pernyi and Nosema bombycis,providing new clues for studying genomic structure of these two microsporidian species.