期刊
NATURE COMMUNICATIONS
卷 11, 期 1, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/s41467-020-15848-y
关键词
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资金
- JS Davies bequest to the University of Adelaide
- Wellcome Trust [108749/Z/15/Z]
- Biotechnology and Biological Sciences Research Council [BB/M011615/1, BB/S020152/1]
- European Molecular Biology Laboratory
- USDA-ARS [3040-31320-012-00D]
- Intramural Research Program of the National Human Genome Research Institute, US National Institutes of Health
- Korean Visiting Scientist Training Award (KVSTA) through the Korea Health Industry Development Institute (KHIDI) - Ministry of Health Welfare [HI17C2098]
- Intramural Research Program of the National Library of Medicine, National Institutes of Health
- Wellcome Trust [108749/Z/15/Z] Funding Source: Wellcome Trust
- BBSRC [BB/S020152/1, BB/M011615/1] Funding Source: UKRI
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [ZIAHG200398] Funding Source: NIH RePORTER
- NATIONAL LIBRARY OF MEDICINE [ZIHLM200888] Funding Source: NIH RePORTER
Inbred 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. Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.
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