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Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

Author

Listed:
  • Colin Kern

    (University of California, Davis)

  • Ying Wang

    (University of California, Davis)

  • Xiaoqin Xu

    (University of California, Davis)

  • Zhangyuan Pan

    (University of California, Davis)

  • Michelle Halstead

    (University of California, Davis)

  • Ganrea Chanthavixay

    (University of California, Davis)

  • Perot Saelao

    (University of California, Davis)

  • Susan Waters

    (University of California, Davis)

  • Ruidong Xiang

    (The University of Melbourne
    Centre for AgriBioscience)

  • Amanda Chamberlain

    (Centre for AgriBioscience)

  • Ian Korf

    (University of California, Davis)

  • Mary E. Delany

    (University of California, Davis)

  • Hans H. Cheng

    (Avian Disease and Oncology Laboratory)

  • Juan F. Medrano

    (University of California, Davis)

  • Alison L. Eenennaam

    (University of California, Davis)

  • Chris K. Tuggle

    (Iowa State University)

  • Catherine Ernst

    (Michigan State University)

  • Paul Flicek

    (European Bioinformatics Institute, Wellcome Genome Campus, Hinxton)

  • Gerald Quon

    (University of California, David)

  • Pablo Ross

    (University of California, Davis)

  • Huaijun Zhou

    (University of California, Davis)

Abstract

Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.

Suggested Citation

  • Colin Kern & Ying Wang & Xiaoqin Xu & Zhangyuan Pan & Michelle Halstead & Ganrea Chanthavixay & Perot Saelao & Susan Waters & Ruidong Xiang & Amanda Chamberlain & Ian Korf & Mary E. Delany & Hans H. C, 2021. "Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22100-8
    DOI: 10.1038/s41467-021-22100-8
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    Cited by:

    1. Zhangyuan Pan & Yuelin Yao & Hongwei Yin & Zexi Cai & Ying Wang & Lijing Bai & Colin Kern & Michelle Halstead & Ganrea Chanthavixay & Nares Trakooljul & Klaus Wimmers & Goutam Sahana & Guosheng Su & M, 2021. "Pig genome functional annotation enhances the biological interpretation of complex traits and human disease," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Changxu Fan & Xiaoyun Xing & Samuel J. H. Murphy & Jennifer Poursine-Laurent & Heather Schmidt & Bijal A. Parikh & Jeesang Yoon & Mayank N. K. Choudhary & Naresha Saligrama & Sytse J. Piersma & Wayne , 2024. "Cis-regulatory evolution of the recently expanded Ly49 gene family," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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