PUBLICATION

High resolution annotation of zebrafish transcriptome using long-read sequencing

Authors
Nudelman, G., Frasca, A., Kent, B., Sadler, K.C., Sealfon, S.C., Walsh, M.J., Zaslavsky, E.
ID
ZDB-PUB-180801-2
Date
2018
Source
Genome research   28(9): 1415-1425 (Journal)
Registered Authors
Kent, Brandon, Sadler Edepli, Kirsten C.
Keywords
none
Datasets
GEO:GSE101843
MeSH Terms
  • Animals
  • Molecular Sequence Annotation*
  • Sequence Analysis, RNA/methods
  • Sequence Analysis, RNA/standards
  • Sequence Homology, Nucleic Acid
  • Transcriptome*
  • Zebrafish/genetics*
PubMed
30061115 Full text @ Genome Res.
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 mir-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping