关键词: 家蚕, 基因组, 转座元件, LTR逆转录转座子, 系统发育分析, 组织表达谱

Abstract: 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.

Key words: Silkworm (Bombyx mori), genome, transposable elements, LTR retrotransposons, phylogenetic analysis, tissue expression profile