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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
ISSN1674-4918
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
DOI10.1111/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
EISSN1759-6831
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
被引频次:36[WOS]   [WOS记录]     [WOS相关记录]
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
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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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