ArticleGenome research2018
High resolution annotation of zebrafish transcriptome using long-read sequencing.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- AltEx-BE: a tool for designing splice-site-targeting gRNAs for base editing-mediated exon skipping with exon-level annotations in diverse experimental animals.Experimental animals · 2026Article
- Molecular Basis of Color Variation in Taiwanese Loach Revealed by Early Developmental Transcriptome Analysis.Animals : an open access journal from MDPI · 2026Article
- High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.BMC biology · 2025Article
- Article
- Full-length transcriptome sequencing and identification of skin colour-associated genes in red tilapia.Journal of genetics · 2025Article
- An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.Communications biology · 2024Article
- Transcriptome Analysis Reveals the Immunosuppression in Tiger Pufferfish (Animals : an open access journal from MDPI · 2024Article
- A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome.G3 (Bethesda, Md.) · 2024Article
- miR-430 regulates zygotic mRNA during zebrafish embryogenesis.Genome biology · 2024Article
- Extensive post-transcriptional regulation revealed by integrative transcriptome and proteome analyses in salicylic acid-induced flowering in duckweed (Frontiers in plant science · 2024Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.Genome biology · 2023Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.bioRxiv : the preprint server for biology · 2023Article
- Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies.BMC genomics · 2023Article
- Comparative Analysis of miRNA-mRNA Regulation in the Testes ofInternational journal of molecular sciences · 2023Article
- Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).G3 (Bethesda, Md.) · 2023Article
- Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica.Marine biotechnology (New York, N.Y.) · 2022Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing.Viruses · 2022Article
- Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish.Frontiers in cell and developmental biology · 2022Article
- Screening and Validation of p38 MAPK Involved in Ovarian Development ofFrontiers in veterinary science · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short-read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835 high-confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology, and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and noncoding RNAs, isoform switching occurrences, and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8-kb transcript spanning multiple
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Registered trials
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