PT  - JOURNAL ARTICLE
AU  - Chengjie Chen
AU  - Junting Feng
AU  - Bo Liu
AU  - Jiawei Li
AU  - Lei Feng
AU  - Xiaoling Yu
AU  - Jixian Zhai
AU  - Blake C. Meyers
AU  - Rui Xia
TI  - sRNAanno --- a database repository of uniformly-annotated small RNAs in plants
AID  - 10.1101/771121
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 771121
4099  - http://biorxiv.org/content/early/2019/09/18/771121.short
4100  - http://biorxiv.org/content/early/2019/09/18/771121.full
AB  - Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Except miRNAs, the other two classes are not well-annotated and collected in public databases for most sequenced plant genomes. We performed comprehensive sRNA annotation for 138 plant species, which have fully sequenced genomes and public next-generation-sequencing (NGS) sRNA data available. The results are available via an online repository called sRNAanno (www.plantsRNAs.org). Compared to plant miRNAs deposited in miRBase, we obtained much more miRNAs, which are more complete and reliable because of consistent and high-stringent criteria used in our miRNA annotation. sRNAanno also provides free access to genomic information for >16,000 PHAS loci and >21,000,000 hc-siRNA loci annotated from these 138 plants. On the basis of Integrative Genomics Viewer (IGV), we developed a visualization tool for browsing NGS sRNA data (IGV-sRNA), which have been integrated a series of new functions compatible to specific sRNA features. To make sRNA annotation an easy task, sRNAanno also provides free service of sRNA annotation to the community. In summary, sRNAanno and IGV-sRNA are great resources to facilitate the genomic and genetic research of plant small RNAs.NGSNext generation sequencing;sRNAssmall RNAs;miRNAsmicroRNAs;siRNAssmall interfering RNAs;phasiRNAphased siRNAs;hc-siRNAsheterochromatic siRNAs;IGVIntegrative Genomics Viewer.