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- Title
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.
- Authors
Low, Wai Yee; Tearle, Rick; Bickhart, Derek M.; Rosen, Benjamin D.; Kingan, Sarah B.; Swale, Thomas; Thibaud-Nissen, Françoise; Murphy, Terence D.; Young, Rachel; Lefevre, Lucas; Hume, David A.; Collins, Andrew; Ajmone-Marsan, Paolo; Smith, Timothy P. L.; Williams, John L.
- 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). Despite technological advances, chromosome-level assemblies of mammalian genomes are still rare. Here, the authors use PacBio, Chicago and Hi-C approaches to generate a highly contiguous and partially-phased genome assembly for the water buffalo, Bubalus bubalis
- Publication
Nature Communications, 2019, Vol 10, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-018-08260-0