TY - JOUR
T1 - sRNAanno—a database repository of uniformly annotated small RNAs in plants
AU - Chen, Chengjie
AU - Li, Jiawei
AU - Feng, Junting
AU - Liu, Bo
AU - Feng, Lei
AU - Yu, Xiaoling
AU - Li, Guanliang
AU - Zhai, Jixian
AU - Meyers, Blake C.
AU - Xia, Rui
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85101820046&partnerID=8YFLogxK
U2 - 10.1038/s41438-021-00480-8
DO - 10.1038/s41438-021-00480-8
M3 - Article
C2 - 33642576
AN - SCOPUS:85101820046
SN - 2052-7276
VL - 8
JO - Horticulture Research
JF - Horticulture Research
IS - 1
M1 - 45
ER -