Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers
文献类型：期刊论文
| 作者 | Pan, Jin ; Wang, Baosheng ; Pei, Zhi-Yong ; Zhao, Wei ; Gao, Jie ; 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 |
| 中文摘要 | 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. |
| 原文出处 | 10.1111/1755-0998.12342 |
| 语种 | 英语 |
| 公开日期 | 2015-07-15 |
| 源URL | [http://ir.xtbg.org.cn/handle/353005/9176]  |
| 专题 | 西双版纳热带植物园_其他 |
| 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：西双版纳热带植物园
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