Zhou Qiu-Zhong, Zhang Bindan, Yu Quan-You, Zhang Ze
Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.
School of Economics and Business Administration, Chongqing University, Campus A, No. 174 Shazheng Rd., Shapingba, Chongqing, 400044, China.
BMC Bioinformatics. 2016 Sep 13;17(1):370. doi: 10.1186/s12859-016-1251-y.
Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori).
In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA.
We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .
长链非编码RNA（lncRNA）可能在高等生物的广泛发育过程中发挥关键作用。最近，lncRNA已在真核生物中被广泛鉴定，并且已经为人类、小鼠、果蝇等开发了许多lncRNA数据库。然而，在唯一完全驯化的昆虫家蚕（Bombyx mori）中，关于它们的信息却很少。
在本研究中，我们使用现有的家蚕RNA测序数据和公共单基因序列系统地扫描lncRNA。最终，我们在家蚕中鉴定并收集了6281个lncRNA。此外，我们还从先前的研究中收集了1986个微小RNA（miRNA）。然后，我们将它们整理成一个基于网络的综合数据库BmncRNAdb。该数据库为数据浏览和在线分析提供了用户友好的界面，以及三个在线工具，供用户预测lncRNA或miRNA的靶基因。
我们系统地鉴定并收集了家蚕lncRNA，并构建了一个家蚕lncRNA和miRNA的综合数据库。这项工作让我们对家蚕lncRNA有了初步了解，并为未来家蚕和其他昆虫的非编码RNA研究奠定了基础。BmncRNAdb可在http://gene.cqu.edu.cn/BmncRNAdb/index.php免费获取。
