TY - JOUR
T1 - Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics
T2 - A case study in Vitaceae
AU - Liu, Bin Bin
AU - Ma, Zhi Yao
AU - Ren, Chen
AU - Hodel, Richard G.J.
AU - Sun, Miao
AU - Liu, Xiu Qun
AU - Liu, Guang Ning
AU - Hong, De Yuan
AU - Zimmer, Elizabeth A.
AU - Wen, Jun
N1 - Publisher Copyright:
© 2021 Institute of Botany, Chinese Academy of Sciences
PY - 2021/9
Y1 - 2021/9
N2 - 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 10× 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.
AB - 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 10× 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.
KW - deep genome skimming
KW - Hyb-Seq
KW - mitochondrial genes
KW - nuclear ribosomal DNA
KW - single-copy nuclear genes
KW - Vitaceae
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U2 - 10.1111/jse.12806
DO - 10.1111/jse.12806
M3 - Article
AN - SCOPUS:85114012588
SN - 1674-4918
VL - 59
SP - 1124
EP - 1138
JO - Journal of Systematics and Evolution
JF - Journal of Systematics and Evolution
IS - 5
ER -