ArticleBMC biology2025
High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.
Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Developmental and tissue expression breadth define distinct but overlapping classes of housekeeping genes.PLoS computational biology · 2026Article
- Transcriptomic Analysis Reveals Multilayer Regulation Underlying Development and Pregnancy in the Malayan Pangolin.Animal genetics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- A Novel CRYBB2 Splicing Mutation Is Associated With Lens Extracellular Matrix Remodeling and Vascular Alterations in Congenital Cataract.Investigative ophthalmology & visual science · 2026Article
- Genome-wide identification of the interferon complex establishes IFNf in Cypriniformes.BMC biology · 2025Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundThe zebrafish has significantly advanced our understanding of human disease and development, with nearly 70% of single-copy protein-coding genes conserved between the species. However, research on zebrafish is limited by gaps in existing genome annotations, which are primarily based on computational predictions and short-read sequencing data.
resultsTo address this issue, we employed the PacBio Sequel II platform to generate a time-series full-length transcriptome landscape of zebrafish embryogenesis, covering 21 time points from embryo to six days post-fertilization. Our analysis uncovered 2113 previously unannotated genes and 33,018 novel isoforms of previously annotated genes, substantially expanding the current zebrafish gene annotations. We verified these findings using various methods, including domain prediction, homology analysis, conservation analysis, transcript quantification with short-read RNA-seq, and promoter position information with H3K4me3 and CAGE-seq. Furthermore, we analyzed the dynamic expression of transcripts across the 21 developmental stages using next-generation sequencing data, identifying variable splicing events throughout these stages.
conclusionsCollectively, our study provides a high-resolution and significantly improved transcriptome annotation during zebrafish embryogenesis, offering a valuable resource for the zebrafish research community.
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