Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome
Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome
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家蚕 (Bombyx mori) 基因组中 TC1/Mariner 的全基因组鉴定和进化
DOI：
10.1007/s13258-018-0648-6
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发表时间：
2018
期刊：
影响因子：
2.1
通讯作者：
Zhang Hua Hao
中科院分区：
文献类型：
--
作者：
Xie Li Qin;Wang Ping Lan;Jiang Shen Hua;Zhang Ze;Zhang Hua Hao
Tc1/Marinine转座子属于第二类转座元件(TES)，利用DNA介导的“剪切粘贴”机制进行转座，几乎在所有生物体中都发现了它们的存在。虽然家蚕(Bombyx Mori)含有大量的Tc1/Marine元件，但该超家族在家蚕中的全基因组信息尚不清楚。在本研究中，我们在家蚕基因组中鉴定了2670TC1/Mariner(Bmmar)元件。利用重复序列分类工具fgCluust将所有的TES分为22个家族，其中7个为本研究首次报道。基于转座酶催化结构域(DDxD/E)的系统发育和结构分析表明，Tc1/Mariner的所有成员被分成5个亚组：Mariner、Tc1、MAT、DD40D和DD41D/E。在这5个亚组中，Tc1/Mariner的成员最多(51.23%)。特别是，系统发育分析和结构分析表明，Bmmar15(DD40D)在昆虫中形成了一个新的Tc1/MarineElement亚群，被称为asbmori。此外，我们得出结论，DD40D似乎介于水手和Tc1之间。最后，我们估计了家蚕Tc1/Marinein每个拷贝的插入时间，发现大多数成员在0到1mya的时间内都得到了显著的扩增。此外，详细的功能数据分析表明，Bmmar1、Bmmar6和Bmmar9具有EST证据和完整的转座酶。这些结果提示Tc1/Marine1可能具有潜在的转座活性。综上所述，本研究为Tc1/Marinein昆虫基因组的景观、起源和进化提供了一些新的见解。
TC1/Marinertransposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount ofTC1/Marinerelements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670TC1/Mariner(Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members ofTC1/Marinerwere grouped into five subgroups:Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups,maTrather thanMarinerpossessed most members ofTC1/Mariner(51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed thatBmmar15(DD40D) formed a new basal subgroup ofTC1/Marinerelement in insects, which was referred to asbmori. Furthermore, we concluded that DD40D appeared to intermediate betweenmarinerandTc1. Finally, we estimated the insertion time for each copy ofTC1/Marinerin the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed thatBmmar1, Bmmar6andBmmar9had EST evidence and intact transposases. These implied thatTC1/Marinermight have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution ofTC1/Marinerin the insect genomes.