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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
Source PublicationSCIENTIFIC REPORTS
Volume6
SubtypeArticle
AbstractNext-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.
DOI10.1038/srep35736
Indexed BySCI
Language英语
WOS IDWOS:000386084200001
Citation statistics
Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/136175
Collection海洋生物技术研发中心
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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).
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