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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 #348469

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

Author
item Low, Wai Yee - University Of Adelaide
item Tearle, Rick - University Of Adelaide
item Bickhart, Derek
item Rosen, Benjamin
item Kingan, Sarah - Pacific Biosciences Inc
item Swale, Thomas - Dovetail Genomics
item Smith, Timothy - Tim
item Williams, John - University Of Adelaide

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Water buffalo (Bubalus bubalis), also known as Asian buffalo, is a globally important species for agriculture. A good reference genome of this species is necessary for understanding its biology, managing genetic diversity, and to apply new genome-based selection methods for genetic improvement. We have previously reported a de novo-assembled genome based on 454 and Illumina short reads. Due to the limitations of using only short reads in the assembly, the publicly available genome consists of 366,983 scaffolds, with a scaffold N50 of 1,412,388 bp and an L50 of 581 scaffolds. Here we report an improved diploid assembly of the same individual (Olimpia) using PacBio Sequel and RSII reads (> 69-fold coverage), assembled with the FALCON-Unzip assembler. Despite using a highly inbred animal with a high homozygosity level, 58% of its genome could be phased with a haplotig N50 of 0.394 Mbp, and the longest haplotig is 2.77 Mbp. Scaffolding using Chicago and HiC reads was done using the Dovetail HiRise software, along with custom scripts to remove false contig breaks that were artificially introduced. Improvement in the latest assembly scaffold N50 is 117,187,264 bp which is 83-fold longer than the previous short read-based assembly, and has an L50 that is made up of only 9 scaffolds. The current draft of the assembly is still evolving as we continue to correct potential misorientation within scaffolds and examine conservation of synteny with the cattle and goat genomes, before final gap filling, assembly polishing, and annotation.