BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.
BACKGROUND
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).


METHODS
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.


CONCLUSIONS
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 .
Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.
Qiu-Zhong
QZ
Zhou
School of Economics and Business Administration, Chongqing University, Campus A, No. 174 Shazheng Rd., Shapingba, Chongqing, 400044, China.
Bindan
B
Zhang
Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.
Quan-You
QY
Yu
Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China. zezhang@cqu.edu.cn.
Ze
Z
Zhang
D000818:Animals; D012831:Bombyx; D030561:Databases, Nucleic Acid; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*
D035683:MicroRNAs; D062085:RNA, Long Noncoding
BmncRNAdb; Long non-coding RNAs; RNA-seq; Silkworm