Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers
文献类型：期刊论文
| 作者 | Pan, Jin2; Wang, Baosheng; Pei, Zhi-Yong; Zhao, Wei2; Gao, Jie5; Mao, Jian-Feng; Wang, Xiao-Ru |
| 刊名 | MOLECULAR ECOLOGY RESOURCES
 |
| 出版日期 | 2015 |
| 卷号 | 15期号:4页码:711-722 |
| 关键词 | conifer genome genotyping-by-sequencing library preparation parameters sequencing depth SNP validation |
| ISSN号 | 1755-098X |
| DOI | 10.1111/1755-0998.12342 |
| 文献子类 | Article |
| 英文摘要 | Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11000 and 14751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking. |
| 学科主题 | Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology |
| 出版地 | HOBOKEN |
| 电子版国际标准刊号 | 1755-0998 |
| WOS关键词 | SNP DISCOVERY ; DE-NOVO ; DNA ; METHYLATION ; FRAMEWORK |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| 语种 | 英语 |
| WOS记录号 | WOS:000356679800004 |
| 出版者 | WILEY |
| 资助机构 | Swedish National Infrastructure for Computing (SNIC) at the High Performance Computing Center North (HPC2N) [SNIC001-12-226, SNIC2013-1-175] ; Formas ; Vetenskapsradet, Sweden |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/25879]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden 3.Beijing Forestry Univ, Natl Engn Lab Forest Tree Breeding, Key Lab Genet & Breeding Forest Trees & Ornamenta, Minist Educ, Beijing 100083, Peoples R China 4.Chinese Acad Sci, Key Lab Trop Forest Ecol, Xishuangbanna Trop Bot Garden, Menglun 666303, Yunnan, Peoples R China 5.Chinese Acad Sci, Beijing Inst Genom, Beijing 100101, Peoples R China 6.Beijing Comp Ctr, Beijing 100094, Peoples R China |
| 推荐引用方式 GB/T 7714 | Pan, Jin,Wang, Baosheng,Pei, Zhi-Yong,et al. Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers[J]. MOLECULAR ECOLOGY RESOURCES,2015,15(4):711-722. |
| APA | Pan, Jin.,Wang, Baosheng.,Pei, Zhi-Yong.,Zhao, Wei.,Gao, Jie.,...&Wang, Xiao-Ru.(2015).Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers.MOLECULAR ECOLOGY RESOURCES,15(4),711-722. |
| MLA | Pan, Jin,et al."Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers".MOLECULAR ECOLOGY RESOURCES 15.4(2015):711-722. |
入库方式： OAI收割
来源：植物研究所
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