sRIS: A Small RNA Illustration System for Plant Next-Generation Sequencing Data Analysis

Area of Science:

• Plant molecular biology
• Bioinformatics
• Genomics

Background:

• Small RNAs (sRNAs), including microRNAs (miRNAs) and short interfering RNAs, regulate gene expression in plants by degrading target messenger RNAs (mRNAs).
• Next-generation sequencing (NGS) has advanced the study of plant sRNA regulatory pathways, leading to the development of numerous bioinformatics tools.
• Existing bioinformatics tools primarily focus on sRNA expression profiling and novel miRNA prediction, often lacking integrated analysis of sRNA target genes, which hinders the study of host-virus interactions.

Purpose of the Study:

• To develop a comprehensive bioinformatics system, the Small RNA Illustration System (sRIS), for detailed analysis of plant sRNAs and their targets.
• To enable the identification of interaction mechanisms between hosts and viruses, as well as synergistic effects between multiple viruses.
• To facilitate easier retrieval and access to analysis outputs, including figures and tables, for efficient result interpretation.

Main Methods:

• Development of the Small RNA Illustration System (sRIS) with two core components: sRNA overview analysis and sRNA target prediction.
• The sRNA overview analysis component identifies miRNAs and investigates virus-derived small interfering RNAs.
• The sRNA target prediction component integrates bioinformatics calculations with degradome sequencing data to enhance prediction accuracy.

Main Results:

• The sRIS system provides a comprehensive platform for analyzing plant sRNAs, including miRNA identification and virus-derived small interfering RNA investigation.
• The system enhances sRNA target prediction accuracy by combining computational methods with experimental degradome sequencing data.
• sRIS facilitates the visualization and quantification of results through easily accessible figures and tables, streamlining data interpretation.

Conclusions:

• The Small RNA Illustration System (sRIS) addresses the limitations of existing tools by integrating sRNA expression analysis with accurate target prediction.
• sRIS is a valuable resource for researchers studying gene expression regulation, host-virus interactions, and synergistic viral effects in plants.
• The system's user-friendly design and comprehensive analysis capabilities make it an efficient tool for plant sRNA research.