ArticleFrontiers in genetics2021
PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- Combined Transcriptomic and Histological Profiling Uncover Hepatic Regulatory Hierarchy of TriploidBiology · 2026Article
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.BMC genomics · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Molecular signatures and machine learning driven stress biomarkers for rainbow trout aquaculture and climate adaptation.Scientific reports · 2025Article
- Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.NAR genomics and bioinformatics · 2025Article
- Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line.Scientific data · 2025Article
- Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.BMC genomics · 2025Review
- An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.Communications biology · 2024Article
- Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout.Animal microbiome · 2024Article
- Characterisation of sRNAs enriched in outer membrane vesicles of pathogenicJournal of extracellular biology · 2024Article
- Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak.BMC genomics · 2024Article
- Single-cell atlas of rainbow trout peripheral blood leukocytes and profiling of their early response to infectious pancreatic necrosis virus.Frontiers in immunology · 2024Article
- Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows.Plant methods · 2023Article
- Full-length transcriptome from different life stages of cobia (Rachycentron canadum, Rachycentridae).Scientific data · 2023Article
- Exploring differential exon usage via short- and long-read RNA sequencing strategies.Open biology · 2022Article
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- Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in
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