PT  - JOURNAL ARTICLE
AU  - Wai Yee Low
AU  - Rick Tearle
AU  - Ruijie Liu
AU  - Sergey Koren
AU  - Arang Rhie
AU  - Derek M. Bickhart
AU  - Benjamin D. Rosen
AU  - Zev N. Kronenberg
AU  - Sarah B. Kingan
AU  - Elizabeth Tseng
AU  - Françoise Thibaud-Nissen
AU  - Fergal J. Martin
AU  - Konstantinos Billis
AU  - Jay Ghurye
AU  - Alex R. Hastie
AU  - Joyce Lee
AU  - Andy W.C. Pang
AU  - Michael P. Heaton
AU  - Adam M. Phillippy
AU  - Stefan Hiendleder
AU  - Timothy P.L. Smith
AU  - John L. Williams
TI  - Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
AID  - 10.1101/720797
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 720797
4099  - http://biorxiv.org/content/early/2019/08/09/720797.short
4100  - http://biorxiv.org/content/early/2019/08/09/720797.full
AB  - We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.