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Updated: Oct 26, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With

Ali Ali¹, Gary H Thorgaard², Mohamed Salem¹

¹Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States.

Frontiers in Genetics

|August 2, 2021

Summary

This study presents the first full-length rainbow trout transcriptome assembly using long-read sequencing, revealing novel transcripts and alternative splicing events. This resource aids understanding of fish growth, disease resistance, and selective breeding.

Keywords:

Iso-Seq PacBio alternative polyadenylation alternative splicing exon usage long reads rainbow trout transcriptome

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Area of Science:

Aquatic Genomics
Transcriptomics
Molecular Biology

Background:

Rainbow trout (Oncorhynchus mykiss) is a key model organism for biological research.
Previous transcriptome studies relied on short-read sequencing, limiting resolution of transcript complexity.

Purpose of the Study:

To generate the first full-length transcriptome assembly of rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq).
To refine and validate the reconstructed transcriptome and improve genome annotation.

Main Methods:

Single-molecule long-read isoform sequencing (Iso-Seq) was employed for transcriptome assembly.
Extensive computational approaches were utilized for transcriptome refinement and validation.

Main Results:

Identified 10,640 novel high-confidence transcripts and 1,479 unmapped isoforms.
Revealed an average of ~3 transcript isoforms per gene locus, with intron retention and exon skipping dominating alternative splicing (56%).
Linked specific alternative splicing events to fish growth, disease resistance (e.g., bacterial cold-water disease), stress response, and migration.

Conclusions:

The Iso-Seq approach significantly enhanced rainbow trout genome annotation.
The reconstructed transcriptome provides valuable resources for future genetics and genomics studies.
Identified transcription events associated with economically important traits offer potential for selective breeding applications.