Han Min-Jin, Zhou Qiu-Zhong, Zhang Hua-Hao, Tong Xiaoling, Lu Cheng, Zhang Ze, Dai Fangyin
State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China.
Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China.
Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw148. Print 2016.
Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. DATABASE URL: http://gene.cqu.edu.cn/iMITEdb/.
微型反向重复转座元件（MITEs）因其在真核生物基因组中的广泛存在和高拷贝数而备受关注。然而，关于昆虫和其他动物中MITEs的系统知识仍然匮乏。在本研究中，我们从98种昆虫物种的基因组中鉴定出6012个MITE家族。将这些MITEs与NCBI非冗余数据库和Repbase中已知的MITEs进行比较，结果显示6012个MITE家族中有5701个（约95%）是新发现的。不同昆虫物种中MITEs的丰度差异极大，且与基因组大小显著相关。一般来说，较大的基因组比较小的基因组包含更多的MITEs。此外，所有鉴定出的MITEs都被纳入了一个新构建的数据库（iMITEdb）（http://gene.cqu.edu.cn/iMITEdb/），该数据库具有浏览、搜索、BLAST和下载等功能。总体而言，我们的研究结果不仅为昆虫MITEs提供了深入见解，还将改善昆虫基因组的组装和注释。更重要的是，本研究呈现的结果将推动昆虫中MITEs功能、进化及应用的研究。数据库网址：http://gene.cqu.edu.cn/iMITEdb/
