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单体型解析基因组为安格斯牛和婆罗门牛的结构变异和基因组成提供了新的见解。

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

机构信息

The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.

出版信息

Nat Commun. 2020 Apr 29;11(1):2071. doi: 10.1038/s41467-020-15848-y.

DOI:10.1038/s41467-020-15848-y
PMID:32350247
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7190621/
Abstract

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.

摘要

近交系动物在历史上被选择用于基因组分析，以避免由单倍型变异引起的组装问题，但这导致了两个基因组的组合。在这里，我们报告了一种单倍型感知的支架和抛光管道，该管道用于创建由三联体 binning 方法生成的重叠群创建的安格斯（黄牛）和婆罗门（印度牛）牛亚种的单倍型分辨率、染色体水平的基因组组装。这些组装揭示了区分亚种的结构和拷贝数变异，并且变体检测对所选的特定参考基因组敏感。与黄牛谱系相比，六个具有免疫相关功能的基因在印度牛中具有额外的拷贝，并且脂肪酸去饱和酶的一个印度牛特异性额外拷贝受到正选择。单倍型基因组还能够使转录本定相以检测等位基因特异性表达。这项工作说明了单倍型分辨率基因组在更好地探索进化和功能变异方面的价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d13cb8dc67d4/41467_2020_15848_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/3e7d384b6613/41467_2020_15848_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/ae82f132f8cf/41467_2020_15848_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d415c50850a6/41467_2020_15848_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d0ea5e493b24/41467_2020_15848_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/3ac48c276103/41467_2020_15848_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d13cb8dc67d4/41467_2020_15848_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/3e7d384b6613/41467_2020_15848_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/ae82f132f8cf/41467_2020_15848_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d415c50850a6/41467_2020_15848_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d0ea5e493b24/41467_2020_15848_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/3ac48c276103/41467_2020_15848_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d56f/7190621/d13cb8dc67d4/41467_2020_15848_Fig6_HTML.jpg

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