Journal ArticleDOI
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
Mingzhou Li,Shilin Tian,Long Jin,Guangyu Zhou,Ying Li,Yuan Zhang,Tao Wang,Carol K.L. Yeung,Lei Chen,Jideng Ma,Jinbo Zhang,Anan Jiang,Ji Li,Chaowei Zhou,Jie Zhang,Yingkai Liu,Xiaoqing Sun,Hongwei Zhao,Zexiong Niu,Pinger Lou,Lingjin Xian,Xiaoyong Shen,Shaoqing Liu,Shunhua Zhang,Mingwang Zhang,Li Zhu,Surong Shuai,Lin Bai,Guoqing Tang,Haifeng Liu,Yanzhi Jiang,Miaomiao Mai,Jian Xiao,Xun Wang,Qi Zhou,Zhiquan Wang,Paul Stothard,Ming Xue,Xiaolian Gao,Zonggang Luo,Yiren Gu,Hongmei Zhu,Xiaoxiang Hu,Yaofeng Zhao,Graham Plastow,Jinyong Wang,Zhi Jiang,Kui Li,Ning Li,Xuewei Li,Ruiqiang Li +50 more
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TLDR
Comparing the genome of Tibetan wild boars with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig.Abstract:
We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.read more
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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas,Steven L. Salzberg,Wei Zhu,Mihaela Pertea,Jonathan E. Allen,Joshua Orvis,Owen White,C R Buell,Jennifer R. Wortman +8 more
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Journal Article
Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen MR, Peltonen L. Nat Genet 2004; 36:371-6.
TL;DR: Familial combined hyperlipidemia (FCHL), characterized by elevated levels of serum total cholesterol, triglycerides or both, is observed in about 20% of individuals with premature coronary heart disease and is linked and associated with the gene encoding upstream transcription factor 1 (USF1) in 60 extended families with FCHL.
Journal ArticleDOI
Extensive error in the number of genes inferred from draft genome assemblies.
James F. Denton,Jose Lugo-Martinez,Abraham E. Tucker,Daniel R. Schrider,Wesley C. Warren,Matthew W. Hahn +5 more
TL;DR: The magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families, and the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, are investigated.
Journal ArticleDOI
Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.
Huashui Ai,Xiaodong Fang,Bin Yang,Zhiyong Huang,Hao Chen,Likai Mao,Feng Zhang,Lu Zhang,Leilei Cui,Weiming He,Jie Yang,Xiaoming Yao,Lisheng Zhou,Lijuan Han,Jing Li,Silong Sun,Xianhua Xie,Boxian Lai,Ying Su,Yao Lu,Hui Yang,Tao Huang,Wenjiang Deng,Rasmus Nielsen,Jun Ren,Lusheng Huang +25 more
TL;DR: An exceptionally large (14-Mb) region with a low recombination rate on the X chromosome is found that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively.
Journal ArticleDOI
Human high-altitude adaptation: forward genetics meets the HIF pathway
Abigail W. Bigham,Frank S. Lee +1 more
TL;DR: High-altitude adaptation may be due to multiple genes that act in concert with one another, and unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia.
References
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