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

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, Andrew Collins, Paolo Ajmone-Marsan, Timothy P. L. Smith and John L. Williams ()
Additional contact information
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

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: 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).

Date: 2019
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DOI: 10.1038/s41467-018-08260-0

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