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Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0.

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

Author information

1
The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
2
Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, WI, 53706, USA.
3
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD, 20705, USA.
4
Pacific Biosciences, Menlo Park, CA, 94025, USA.
5
Dovetail Genomics, Santa Cruz, CA, 95060, USA.
6
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
7
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
8
Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Queensland, 4102, Australia.
9
Genetic Epidemiology and Bioinformatics, University of Southampton, Southampton, SO16 6YD, UK.
10
Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, PC, Italy.
11
US Meat Animal Research Center, ARS USDA, Clay Center, Ne, 68933, USA.
12
The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia. john.williams01@adelaide.edu.au.

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).

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