PigVar: a database of pig variations and positive selection signatures
文献类型：期刊论文
| 作者 | Liu YH4; Otecko NO2,6; Zhang YP*4,6,7; Zhou ZY3,6; Wang L4; Xie HB6; Irwin DM5,6; Adeola AC6; Zhang JY1; Li AM7 |
| 刊名 | Database
 |
| 出版日期 | 2017 |
| 卷号 | **期号:**页码:1-10 |
| 英文摘要 | Pigs are excellent large-animal models for medical research and a promising organ donor source for transplant patients. Next-generation sequencing technology has yielded a dramatic increase in the volume of genomic data for pigs. However, the limited amount of variation data provided by dbSNP, and non-congruent criteria used for calling variation, present considerable hindrances to the utility of this data. We used a uniform pipeline, based on GATK, to identify non-redundant, high-quality, whole-genome SNPs from 280 pigs and 6 outgroup species. A total of 64.6 million SNPs were identified in 280 pigs and 36.8 million in the outgroups. We then used LUMPY to identify a total of 7 236 813 structural variations (SVs) in 211 pigs. Positively selected loci were identified through five statistical tests of different evolutionary attributes of the SNPs. Combining the non-redundant variations and the evolutionary selective scores, we built the first pig-specific variation database, PigVar (http://www.ibiomedical.net/pigvar/), which is a web-based open-access resource. PigVar collects parameters of the variations including summary lists of the locations of the variations within protein-coding and long intergenic non-coding RNA (lincRNA) genes, whether the SNPs are synonymous or non-synonymous, their ancestral and derived states, geographic sampling locations, as well as breed information. The PigVar database will be kept operational and updated to facilitate medical research using the pig as model and agricultural research including pig breeding. |
| 语种 | 英语 |
| 资助机构 | This work was supported the Ministry of Agriculture of China (2016ZX08009-003-006); and the National Natural Science Foundation of China (31061160189 and U1534208); and the National 973 Program of China (2013CB835203); and the Doctoral Scientific Research Foundation of Xi’an University of Technology (112-451116001). ; This work was supported the Ministry of Agriculture of China (2016ZX08009-003-006); and the National Natural Science Foundation of China (31061160189 and U1534208); and the National 973 Program of China (2013CB835203); and the Doctoral Scientific Research Foundation of Xi’an University of Technology (112-451116001). |
| 源URL | [http://159.226.149.26:8080/handle/152453/12065]  |
| 专题 | 昆明动物研究所_遗传资源与进化国家重点实验室 昆明动物研究所_分子进化基因组学 |
| 作者单位 | 1.School of Computer Science and Technology, Xidian University, Xi’an, Shaanxi 710071, China 2.Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China 3.School of Computer Science and Engineering, Xi’an University of Technology, Xi’an, Shaanxi 710048, China 4.Laboratory for Conservation and Utilization of Bioresource, Yunnan University, Kunming 650091, China 5.Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada 6.State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Chin 7.Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China |
| 推荐引用方式 GB/T 7714 | Liu YH,Otecko NO,Zhang YP*,et al. PigVar: a database of pig variations and positive selection signatures[J]. Database,2017,**(**):1-10. |
| APA | Liu YH.,Otecko NO.,Zhang YP*.,Zhou ZY.,Wang L.,...&Li AM.(2017).PigVar: a database of pig variations and positive selection signatures.Database,**(**),1-10. |
| MLA | Liu YH,et al."PigVar: a database of pig variations and positive selection signatures".Database **.**(2017):1-10. |
入库方式： OAI收割
来源：昆明动物研究所
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