An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

  1. Nathan D Lawson  Is a corresponding author
  2. Rui Li
  3. Masahiro Shin
  4. Ann Grosse
  5. Onur Yukselen
  6. Oliver A Stone
  7. Alper Kucukural
  8. Lihua Zhu
  1. University of Massachusetts Medical School, United States
  2. University of Oxford, United Kingdom

Abstract

The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.

Data availability

All data generated in this study are available in accompanying source data files. Transcriptome annotation files described in this study are available for download at zf-transcriptome.umassmed.edu. Raw and processed RNA-seq data generated in this study are available at GEO (GSE152759).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Nathan D Lawson

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    For correspondence
    nathan.lawson@umassmed.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7788-9619
  2. Rui Li

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Masahiro Shin

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ann Grosse

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Onur Yukselen

    Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Oliver A Stone

    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Alper Kucukural

    Department of Bioinformatic and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9983-394X
  8. Lihua Zhu

    Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Heart, Lung, and Blood Institute (R35HL140017)

  • Nathan D Lawson

National Human Genome Research Institute (U01HG007910)

  • Onur Yukselen
  • Alper Kucukural

National Center for Advancing Translational Sciences (UL1TR001453)

  • Onur Yukselen
  • Alper Kucukural

National Institute of Neurological Disorders and Stroke (R21NS105654)

  • Nathan D Lawson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Zebrafish studies were performed in accordance with protocols #A2613 and #A2632 approved by the University of Massachusetts institutional animal care and use committee (IACUC).

Reviewing Editor

  1. Elisabeth Busch-Nentwich, University of Cambridge

Publication history

  1. Received: February 6, 2020
  2. Accepted: August 21, 2020
  3. Accepted Manuscript published: August 24, 2020 (version 1)
  4. Version of Record published: September 11, 2020 (version 2)

Copyright

© 2020, Lawson et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Nathan D Lawson
  2. Rui Li
  3. Masahiro Shin
  4. Ann Grosse
  5. Onur Yukselen
  6. Oliver A Stone
  7. Alper Kucukural
  8. Lihua Zhu
(2020)
An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
eLife 9:e55792.
https://doi.org/10.7554/eLife.55792

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