iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects
iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects
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iMITEdb：昆虫微型反向重复转座元件的全基因组景观
DOI：
10.1093/database/baw148
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发表时间：
2016-12-26
影响因子：
5.8
通讯作者：
Dai, Fangyin
中科院分区：
文献类型：
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作者：
Han, Min-Jin;Zhou, Qiu-Zhong;Dai, Fangyin
微型反向重复转座元件（MITEs）由于其在真核生物基因组中的广泛存在和高拷贝数而受到广泛关注。然而，对昆虫和其他动物中的MITE的系统知识仍然缺乏。在这项研究中，我们确定了6012螨家庭从98种昆虫基因组。将这些MITE与NCBI非冗余数据库和Repbase中的已知MITE进行比较，发现6012个MITE家族中有5701个（约95%）是新的。MITE的丰度在不同的昆虫物种之间变化很大，并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MITE。此外，所有鉴定的MITE均被纳入新构建的数据库（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提供了对昆虫MITE的深入了解，而且还将改善昆虫基因组的组装和注释。更重要的是，本研究的结果将促进昆虫MITES功能、进化和应用的研究。数据库URL：http://gene.cqu.edu.cn/iMITEdb/
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/