sRNAanno

sRNAanno annotates small RNAs in plants by providing uniform annotations of microRNAs (miRNAs), phased small interfering RNAs (phasiRNAs), and heterochromatic siRNAs (hc-siRNAs) across 138 plant species with fully sequenced genomes using publicly available next-generation sequencing (NGS) sRNA data.

Key Features:

• Extensive Annotation: Annotates microRNAs (miRNAs), phased small interfering RNAs (phasiRNAs), and heterochromatic siRNAs (hc-siRNAs) using consistent, high-stringency annotation criteria and references miRNA content relative to miRBase.
• Large-Scale Data Integration: Includes annotations encompassing over 16,000 PHAS loci and more than 21 million hc-siRNA loci across the annotated plant species.
• Visualization Tool (IGV-sRNA): Provides IGV-sRNA, a specialized visualization module built on the Integrative Genomics Viewer (IGV) with functions tailored to small RNA features.

Scientific Applications:

• Gene regulation studies: Investigating regulatory roles of small RNAs, including miRNAs and phasiRNAs, in plant gene expression.
• Epigenetics: Examining hc-siRNA-associated epigenetic modifications and pathways.
• Development and stress response research: Dissecting molecular mechanisms by which small RNAs influence plant development and responses to stress.
• Comparative and evolutionary analyses: Enabling cross-species comparisons of sRNA repertoires to study sRNA evolution and function across diverse plants.

Methodology:

Annotations were produced from publicly available next-generation sequencing (NGS) sRNA data across 138 plant species with fully sequenced genomes using consistent, high-stringency annotation criteria; IGV-sRNA is implemented on the Integrative Genomics Viewer (IGV) for visualization.