Plant

Plant annotates and catalogs over 2.7 million small RNA (sRNA) loci, including microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs), across 47 plant species to support comparative and regulatory genomics.

Key Features:

• Standardized bioinformatic pipeline: Employs a standardized bioinformatic pipeline to ensure consistent and reliable annotation across different sRNA-seq datasets.
• Annotation scope: Provides detailed annotations for over 2.7 million sRNA loci derived from 1,333 sRNA-seq libraries totaling over 20 billion reads from 47 plant species.
• 24 Nucleotide siRNAs: 24 nucleotide-dominated siRNA loci are primarily located in intergenic regions, particularly at the 5’-flanking regions of protein-coding genes.
• 21 Nucleotide siRNAs: 21 nucleotide-dominated siRNA loci typically originate from double-stranded RNA precursors derived from spliced mRNAs and are prevalent among genic loci from disease resistance genes, especially in monocots.
• Conservation patterns: Indicates that individual siRNA sequences exhibit minimal conservation across species while mature miRNAs tend to be more conserved.
• siRNA annotation advancement: Addresses historically limited siRNA locus annotations by substantially expanding endogenous siRNA locus annotations.

Scientific Applications:

• sRNA conservation analysis: Enables exploration of sRNA sequence and locus conservation across plant species for evolutionary and comparative studies.
• Gene expression regulation studies: Supports investigation of miRNA and siRNA roles in post-transcriptional and transcriptional regulation of gene expression.
• Disease resistance research: Facilitates analysis of 21 nucleotide-dominated siRNA loci associated with disease resistance genes, informing studies of plant immunity mechanisms.

Methodology:

Processes large-scale sRNA-seq data through a standardized bioinformatic pipeline to identify and annotate miRNA and siRNA loci.