Abstract
AbstractInbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry
Reference62 articles.
1. Park, S. D. E. et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 16, 234 (2015).
2. Verdugo, M. P. et al. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 365, 173–176 (2019).
3. Naik, S. N. Origin and domestication of Zebu cattle (Bos indicus). J. Hum. Evol. 7, 23–30 (1978).
4. Koufariotis, L. et al. Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled. Sci. Rep. 8, 17761 (2018).
5. American Brahman Breeders Association. Available at https://brahman.org (2020).
Cited by
89 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献