sRNAanno—a database repository of uniformly annotated small RNAs in plants

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.

Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

“…SNP density and nucleotide diversity were calculated only for SNPs extracted from the 'Feizixiao' VCF file. Similarly, sRNA and LTR densities were calculated from small RNA annotation 73 and LTR annotation files, respectively. All the above 'Feizixiao' genome features were viewed in Circos plotted using TBtools 68 .…”

Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)

“…A total of 134 miRNA-encoding genes were identified in the present dataset ( Figure 2 ) [ 21 ], representing 30 recognized MIRNA gene families. Database comparisons revealed that 109 of the 134 genes had been previously identified in oil palm ( accessed on 5 January 2022), whereas the remaining 25 genes were previously unreported in this species.…”

Biogenesis, Trafficking, and Function of Small RNAs in Plants

“…Its biogenesis also requires RNA Pol IV-mediated transcription and RDR2-mediated formation of dsRNA ( Parent et al, 2015 ). Finally, DCL3 processes the dsRNA into 24 nt siRNA duplexes, and HEN1 methylates the siRNA duplexes to form 24 nt hcsiRNA ( Chen et al, 2021a ; Figure 1C ). Biosynthesis of vsiRNA also requires the participation of DCLs, AGOs, and RDR proteins.…”

“…However, how to distinguish the origin of sRNA in this integral system has become a problem because both plants and fungal pathogens can produce sRNA. The genomes of most species have been sequenced, so the source of sRNA can usually be determined by homology search ( Chen et al, 2021a ). Using a sequential protoplast preparation method to purify fungal protoplasts from infected plant tissues, sRNAs that are transported from plant to fungal pathogen were identified ( Cai et al, 2018 ).…”