April 21, 2020  |  

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

Authors: Low, Wai Yee and Tearle, Rick and Bickhart, Derek M and Rosen, Benjamin D and Kingan, Sarah B and Swale, Thomas and Thibaud-Nissen, Françoise and Murphy, Terence D and Young, Rachel and Lefevre, Lucas and Hume, David A and Collins, Andrew and Ajmone-Marsan, Paolo and Smith, Timothy P L and Williams, John L

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).

Journal: Nature communications
DOI: 10.1038/s41467-018-08260-0
Year: 2019

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