Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
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单倍型解析的牛基因组为结构变异和适应提供了见解
DOI：
10.1101/720797
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
J. Williams
中科院分区：
文献类型：
--
作者：
W. Low;R. Tearle;Ruijie Liu;S. Koren;A. Rhie;D. Bickhart;B. Rosen;Zev N. Kronenberg;S. Kingan;Elizabeth Tseng;F. Thibaud;Fergal J. Martin;Konstantinos Billis;Jay Ghurye;A. Hastie;Joyce Lee;A. Pang;M. P. Heaton;A. Phillippy;S. Hiendleder;T. Smith;J. Williams
我们展示了代表牛磺酸和印度牛的高质量、分阶段的基因组组合，这两个亚种在生产力相关特征和环境适应方面存在显著差异。我们报告了一种新的单倍型感知脚手架和抛光管道，使用三组分方法产生的重叠群来产生安格斯(牛磺酸)和婆罗曼(印度)牛品种的单倍型分辨、染色体水平的基因组组件。这些组合被用来鉴定区分亚种的结构和拷贝数变异，我们发现变异检测对所选择的特定参考基因组很敏感。6个具有免疫相关功能的基因家族在该基因谱系中得到了扩展。从单个个体组装两个亚种的基因组使转录能够分阶段进行，以检测等位基因的特定表达，并研究全基因组的选择性扫描。一个特定于印度的额外的脂肪酸脱饱和酶拷贝正在进行正选择，这可能有助于水稻对高温和干旱的适应。
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.
影响因子：
7
作者：
Bickhart, Derek M.;Hou, Yali;Liu, George E.
通讯作者：
Liu, George E.
影响因子：
56.9
作者：
Verdugo, Marta Pereira;Mullin, Victoria E.;Bradley, Daniel G.
通讯作者：
Bradley, Daniel G.
奇瓦瓦沙漠放牧的多胎安格斯牛和婆罗门牛的代谢特征。
影响因子：
3.3
作者：
Obeidat,BS;Thomas,MG;Hallford,DM;Keisler,DH;Petersen,MK;Bryant,WD;Garcia,MD;Narro,L;Lopez,R
通讯作者：
Lopez,R