家蚕LTR逆转录转座子的鉴定、分类及系统发育分析

Characterization,classification and phylogenetic analysis of long terminal repeat retrotransposons in the silkworm,Bombyx mori

转座子是真核生物基因组的重要组成成分。为了研究家蚕Bombyx mori长末端重复序列(long terminal repeat,LTR)逆转录转座子的分类及进化,本研究采用denovo预测和同源性搜索相结合的方法,在家蚕基因组中共鉴定出了38个LTR逆转录转座子家族,序列长度占整个基因组的0.64%,远小于先前预测的11.8%,其中有6个家族为本研究的新发现。38个家族中,26个家族有表达序列标签(expression sequencetag,EST)证据,表明这些家族具有潜在的活性。对有EST证据的6个家族和没有EST证据的5个家族用RT-PCR进行了组织表达谱实验,结果表明这11个家族在一些组织中有表达,这进一步证实了这些家族具有转录活性,基于此我们推测家蚕中大部分的LTR逆转录转座子家族很可能具有潜在活性。对转座子的插入时间进行估计,结果表明绝大部分元件都是最近1百万年内插入到家蚕基因组中的。我们还比较了黑腹果蝇Drosophila melanogaster、冈比亚按蚊Anopheles gambiae和家蚕B.mori中Ty3/Gypsy超家族分支的差异,结果表明不同枝在不同昆虫中有着不同的扩张。家蚕中LTR逆转录转座子的鉴定和系统分析有助于我们理解逆转录转座子在昆虫进化中的作用。

In eukaryotes,transposable elements（TEs） constitute a large fraction of a genome.TEs are usually classified into two classes based on their transposition mechanisms.ClassⅠ elements use an RNA-mediated mode of transposition,while classⅡ elements（transposons） use a DNA-mediated mode of ＂cut and paste＂ transposition.ClassⅠ elements are further divided into two subclasses：the elements that are characterized by long terminal repeats（LTR retrotransposons） and the elements that lack terminal repeats（non-LTR retrotransposons）.In order to reveal the classification and evolution of LTR retrotransposons,we identified LTR retrotransposons in the domesticated silkworm（Bombyx mori） using de novo and homology search approaches and found 38 families in the silkworm genome,of which 6 families are novel.The sequences of these families constitute 0.64% of the whole genome,which is much less than that previously reported.We also found that 26 of 38 families have EST evidence,implying that they had potential activity.Then RT-PCR was performed to validate the expressions of 11 families（6 families have EST evidence and 5 families have no EST evidence）,and the results showed that these 11 families were expressed in some tissues,further supporting their transcriptional activities.Based on these results,we speculated that most of LTR retrotransposon families in the silkworm genome have potential activity.We estimated the insertion time of LTR retrotransposons,and found that most of them were inserted into the silkworm genome within the past million years.A comparison of Ty3/Gypsy superfamily in Drosophila melanogaster,Anopheles gambiae and B.mori showed that this superfamily experienced different expansion patterns.Given the importance of LTR retrotransposon activity in the evolution of other genomes,our results provide some insights into the roles of LTR in insect genome evolution.