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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

Author

Listed:
  • Wai Yee Low

    (University of Adelaide)

  • Rick Tearle

    (University of Adelaide)

  • Derek M. Bickhart

    (Cell Wall Biology and Utilization Laboratory, ARS USDA)

  • Benjamin D. Rosen

    (Animal Genomics and Improvement Laboratory, ARS USDA)

  • Sarah B. Kingan

    (Pacific Biosciences)

  • Thomas Swale

    (Dovetail Genomics)

  • Françoise Thibaud-Nissen

    (National Institutes of Health)

  • Terence D. Murphy

    (National Institutes of Health)

  • Rachel Young

    (University of Edinburgh, Easter Bush)

  • Lucas Lefevre

    (University of Edinburgh, Easter Bush)

  • David A. Hume

    (Translational Research Institute, Woolloongabba)

  • Andrew Collins

    (University of Southampton)

  • Paolo Ajmone-Marsan

    (Università Cattolica del Sacro Cuore)

  • Timothy P. L. Smith

    (ARS USDA, Clay Center)

  • John L. Williams

    (University of Adelaide)

Abstract

Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was haplotype-phased by FALCON-Unzip. This new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold and contains only 383 gaps. It surpasses the human and goat references in sequence contiguity and facilitates the annotation of hard to assemble gene clusters such as the major histocompatibility complex (MHC).

Suggested Citation

  • Wai Yee Low & Rick Tearle & Derek M. Bickhart & Benjamin D. Rosen & Sarah B. Kingan & Thomas Swale & Françoise Thibaud-Nissen & Terence D. Murphy & Rachel Young & Lucas Lefevre & David A. Hume & Andre, 2019. "Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-08260-0
    DOI: 10.1038/s41467-018-08260-0
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    Cited by:

    1. Ting-Ting Li & Tian Xia & Jia-Qi Wu & Hao Hong & Zhao-Lin Sun & Ming Wang & Fang-Rong Ding & Jing Wang & Shuai Jiang & Jin Li & Jie Pan & Guang Yang & Jian-Nan Feng & Yun-Ping Dai & Xue-Min Zhang & Ta, 2023. "De novo genome assembly depicts the immune genomic characteristics of cattle," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Xue Gao & Sheng Wang & Yan-Fen Wang & Shuang Li & Shi-Xin Wu & Rong-Ge Yan & Yi-Wen Zhang & Rui-Dong Wan & Zhen He & Ren-De Song & Xin-Quan Zhao & Dong-Dong Wu & Qi-En Yang, 2022. "Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. A. Talenti & J. Powell & J. D. Hemmink & E. A. J. Cook & D. Wragg & S. Jayaraman & E. Paxton & C. Ezeasor & E. T. Obishakin & E. R. Agusi & A. Tijjani & W. Amanyire & D. Muhanguzi & K. Marshall & A. F, 2022. "A cattle graph genome incorporating global breed diversity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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