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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #355523

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

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

item YEE LOW, WAI - University Of Adelaide
item TEARLE, RICK - University Of Adelaide
item Bickhart, Derek
item Rosen, Benjamin - Ben
item KINGAN, SARAH - Pacific Biosciences Inc
item SWALE, THOMAS - Dovetail Genomics
item THIBAUD-NISSEN, FRANCOISE - National Center For Biotechnology Information (NCBI)
item MURPHY, TERENCE - National Center For Biotechnology Information (NCBI)
item YOUNG, RACHEL - University Of Edinburgh
item LEFEVRE, LUCAS - University Of Edinburgh
item HUME, DAVID - University Of Queensland
item COLLINS, ANDREW - University Of Southampton
item AJMONE-MARSAN, PAOLO - Università Cattolica Del Sacro Cuore
item Smith, Timothy - Tim
item WILLIAMS, JOHN - University Of Adelaide

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2018
Publication Date: 1/16/2019
Citation: Yee Low, W., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T., Young, R., Lefevre, L., Hume, D., Collins, A., Ajmone-Marsan, P., Smith, T.P., Williams, J. 2019. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications. 10:260.

Interpretive Summary: Water buffalo are a dairy livestock species that thrive in warm and humid climates. Mozzarella and other cheeses made from water buffalo milk have a distinctive flavor and are valued in Italian cuisine. Unlike in dairy cattle, geneticists that study water buffalo do not have the tools necessary to breed for animals that produce more milk. This study provides a genetic tool to water buffalo researchers that rivals the quality of the tools available for dairy cattle.

Technical 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. The 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 could be haplotye-phased by FALCON-Unzip. The new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold with 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).