| Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology | |
| Song, Kai1,2,3; Li, Li1,2,3; Zhang, Guofan1,3,4 | |
| 2016-10-20 | |
| 发表期刊 | SCIENTIFIC REPORTS
 |
| 卷号 | 6 |
| 文章类型 | Article |
| 摘要 | Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling rate and accuracy as a function of coverage. Having initially identified the appropriate parameter settings for filtering to ensure genotype accuracy, we used two different single-nucleotide polymorphism (SNP) calling pipelines, single-sample and multi-sample. We found that a coverage of 15 x was suitable for obtaining sufficient numbers of SNPs with high accuracy. Our work provides guidelines for the selection of sequence coverage when using NGS to investigate species with a high degree of heterozygosity and rapid decay of linkage disequilibrium. |
| DOI | 10.1038/srep35736 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000386084200001 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 版本 | 出版稿 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/136175 |
| 专题 | 海洋生物技术研发中心 |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Shandong, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao 266071, Shandong, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Shandong, Peoples R China 4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266071, Shandong, Peoples R China |
| 第一作者单位 | 中国科学院海洋研究所 |
| 推荐引用方式 GB/T 7714 | Song, Kai,Li, Li,Zhang, Guofan. Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology[J]. SCIENTIFIC REPORTS,2016,6. |
| APA | Song, Kai,Li, Li,&Zhang, Guofan.(2016).Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.SCIENTIFIC REPORTS,6. |
| MLA | Song, Kai,et al."Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology".SCIENTIFIC REPORTS 6(2016). |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Coverage recommendat（633KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
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