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Article|01 Mar 2021|OPEN
sRNAanno—a database repository of uniformly annotated small RNAs in plants
Chengjie Chen1,2,3,4, Jiawei Li1,2,3,4, Junting Feng1,2,3,4, Bo Liu1,2,3,4, Lei Feng1,2,3,4, Xiaoling Yu1,2,3,4, Guanliang Li1,2,3,4, Jixian Zhai 5, Blake C. Meyers6,7 & Rui Xia1,2,3,4,
1State Key Laboratory for Conservation and Utilization of Subtropical AgroBioresources, South China Agricultural University, Guangzhou, China
2Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
3Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510640, China
4Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Chen et al. Horticulture Research (2021) 8:45 Page 7 of 8 Guangdong 510640, China
5Department of Biology & Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
6Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
7Division of Plant Sciences, University of Missouri–Columbia, Columbia, MO 65211, USA

Horticulture Research 8,
Article number: 45 (2021)
doi: 10.1038/hortres.2021.45
Views: 257

Received: 13 Jul 2020
Revised: 06 Nov 2020
Accepted: 13 Dec 2020
Published online: 01 Mar 2021

Abstract

Small RNAs (sRNAs) are essential regulatory molecules, and there are three major sRNA classes in plants: microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Excluding miRNAs, the other two classes are not well annotated or available in public databases for most sequenced plant genomes. We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available. The results are available via an online repository called sRNAanno (www.plantsRNAs.org). Compared with other public plant sRNA databases, we obtained was much more miRNA annotations, which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations. sRNAanno also provides free access to genomic information for >22,721 PHAS loci and >22 million hc-siRNA loci annotated from these 143 plant species. Both miRNA and PHAS loci can be easily browsed to view their main features, and a collection of archetypal trans-acting siRNA 3 (TAS3) genes were annotated separately for quick access. To facilitate the ease of sRNA annotation, sRNAanno provides free service for sRNA annotations to the community. In summary, the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.