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Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae | |
Liu, Bin-Bin; Ma, Zhi-Yao; Ren, Chen3,4; Hodel, Richard G. J.; Sun, Miao5; Liu, Xiu-Qun; Liu, Guang-Ning; Hong, De-Yuan; Zimmer, Elizabeth A.; Wen, Jun2 | |
2021 | |
发表期刊 | JOURNAL OF SYSTEMATICS AND EVOLUTION |
ISSN | 1674-4918 |
卷号 | 59期号:5页码:1124-1138 |
摘要 | With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 data sets with different sequencing coverage in silico. We tested the performance of four data sets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10x coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large data sets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach. |
关键词 | deep genome skimming Hyb-Seq mitochondrial genes nuclear ribosomal DNA single-copy nuclear genes Vitaceae |
学科领域 | Plant Sciences |
DOI | 10.1111/jse.12806 |
收录类别 | SCI |
语种 | 英语 |
WOS关键词 | MITOCHONDRIAL-DNA ; READ ALIGNMENT ; CHLOROPLAST ; EVOLUTION ; VITIS ; GENERATION ; INFERENCE ; THOUSANDS ; PROGRESS ; ACCURACY |
WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
WOS记录号 | WOS:000691707500001 |
出版者 | WILEY |
文献子类 | Article |
出版地 | HOBOKEN |
EISSN | 1759-6831 |
资助机构 | National Natural Science Foundation of China [32000163, 31620103902] ; Smithsonian DNA Barcode Network |
作者邮箱 | WENJ@si.edu |
作品OA属性 | Green Submitted |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/26304 |
专题 | 系统与进化植物学国家重点实验室 |
作者单位 | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change LVEC, Beijing 100093, Peoples R China 3.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, POB 37012, Washington, DC 20013 USA 4.Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable, Guangzhou 510650, Peoples R China 5.Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Peoples R China 6.Aarhus Univ, Dept Biol Ecoinformat & Biodivers, DK-8000 Aarhus C, Denmark 7.Huazhong Agr Univ, Coll Hort & Forestry Sci, Minist Educ, Key Lab Hort Plant Biol, Wuhan 430070, Peoples R China 8.Tongji Univ, Coll Architecture & Urban Planning, Shanghai 200092, Peoples R China |
推荐引用方式 GB/T 7714 | Liu, Bin-Bin,Ma, Zhi-Yao,Ren, Chen,et al. Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae[J]. JOURNAL OF SYSTEMATICS AND EVOLUTION,2021,59(5):1124-1138. |
APA | Liu, Bin-Bin.,Ma, Zhi-Yao.,Ren, Chen.,Hodel, Richard G. J..,Sun, Miao.,...&Wen, Jun.(2021).Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae.JOURNAL OF SYSTEMATICS AND EVOLUTION,59(5),1124-1138. |
MLA | Liu, Bin-Bin,et al."Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae".JOURNAL OF SYSTEMATICS AND EVOLUTION 59.5(2021):1124-1138. |
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