Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Developmental Biology

Background:

• RNA sequencing (RNA-seq) is a powerful tool for transcriptome analysis.
• Analyzing RNA-seq data in non-model organisms is challenging due to a lack of functional annotation.
• Existing tools often require multiple platforms, complicating analysis.

Purpose of the Study:

• To develop a comprehensive, one-stop RNA sequencing analysis pipeline for non-model organisms.
• To enable functional annotation, non-coding RNA identification, and alternative splicing analysis.
• To provide a user-friendly solution for researchers working with Illumina platform RNA-seq data.

Main Methods:

• Development of PipeOne-NM, an integrated RNA-seq analysis pipeline.
• Application of PipeOne-NM to 237 RNA-seq runs from *Schmidtea mediterranea*.
• Analysis included transcriptome assembly, gene/non-coding RNA identification, and co-expression analysis.

Main Results:

• Assembled a transcriptome with 84,827 sequences from 49,320 genes.
• Identified 64,582 mRNAs, 20,217 long non-coding RNAs (lncRNAs), and 3,481 circular RNAs (circRNAs).
• Discovered 1,319 lncRNAs co-expressed with mRNAs and identified differential gene expression related to sexual reproduction and nerve impulse conduction.

Conclusions:

• PipeOne-NM provides a comprehensive platform for transcriptome analysis in non-model organisms.
• The pipeline facilitates functional annotation and identification of various RNA types.
• Results highlight the utility of PipeOne-NM for uncovering biological insights in understudied species.