植物多样性 2018, 40(04) 158-164 DOI:   10.1016/j.pld.2018.06.005  ISSN: 2095-0845 CN: 53-1217/Q

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Plant phylogenomics
Next-generation sequencing
Whole-genome sequencing
Genome skimming
RAD-Seq
Targeted capture
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PubMed
Plant phylogenomics based on genome-partitioning strategies: Progress and prospects
Xiangqin Yua, Dan Yanga,c, Cen Guob,c, Lianming Gaoa
a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
c Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
摘要

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genomepartitioning approaches in plant phylogenomics:genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

关键词 Plant phylogenomics   Next-generation sequencing   Whole-genome sequencing   Genome skimming   RAD-Seq   Targeted capture  
Plant phylogenomics based on genome-partitioning strategies: Progress and prospects
Xiangqin Yua, Dan Yanga,c, Cen Guob,c, Lianming Gaoa
a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
c Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
Abstract:

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genomepartitioning approaches in plant phylogenomics:genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

Keywords: Plant phylogenomics   Next-generation sequencing   Whole-genome sequencing   Genome skimming   RAD-Seq   Targeted capture  
收稿日期 2018-04-24 修回日期 2018-06-27 网络版发布日期  
DOI: 10.1016/j.pld.2018.06.005
基金项目:

This study was supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No:2017-LSFGBOWS-01), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), and the Program of Science and Technology Talents Training of Yunnan Province (2017HA014).

通讯作者: Lianming Gao
作者简介:
作者Email: gaolm@mail.kib.ac.cn

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