Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
文献类型：期刊论文
| 作者 | Liu, Bin-Bin; Ma, Zhi-Yao; Ren, Chen3,4; Hodel, Richard G. J.; Sun, Miao2; Liu, Xiu-Qun; Liu, Guang-Ning; Hong, De-Yuan; Zimmer, Elizabeth A.; Wen, Jun5 |
| 刊名 | JOURNAL OF SYSTEMATICS AND EVOLUTION
 |
| 出版日期 | 2021 |
| 卷号 | 59期号:5页码:1124-1138 |
| 关键词 | deep genome skimming Hyb-Seq mitochondrial genes nuclear ribosomal DNA single-copy nuclear genes Vitaceae |
| ISSN号 | 1674-4918 |
| DOI | 10.1111/jse.12806 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Plant Sciences |
| 出版地 | HOBOKEN |
| 电子版国际标准刊号 | 1759-6831 |
| 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) |
| 语种 | 英语 |
| WOS记录号 | WOS:000691707500001 |
| 出版者 | WILEY |
| 资助机构 | National Natural Science Foundation of China [32000163, 31620103902] ; Smithsonian DNA Barcode Network |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/26304]  |
| 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.Huazhong Agr Univ, Coll Hort & Forestry Sci, Minist Educ, Key Lab Hort Plant Biol, Wuhan 430070, Peoples R China 2.Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Peoples R China 3.Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable, Guangzhou 510650, Peoples R China 4.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, POB 37012, Washington, DC 20013 USA 5.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change LVEC, Beijing 100093, Peoples R China 6.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 7.Aarhus Univ, Dept Biol Ecoinformat & Biodivers, DK-8000 Aarhus C, Denmark 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. |
入库方式： OAI收割
来源：植物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。