石松类和蕨类植物质体基因组结构演化研究进展

doi:10.17520/biods.2019113

生物多样性 ›› 2019, Vol. 27 ›› Issue (11): 1172-1183. DOI: 10.17520/biods.2019113

所属专题：物种形成与系统进化

石松类和蕨类植物质体基因组结构演化研究进展

杜新宇^1,²,卢金梅^1,^*(),李德铢^1,²

1 中国科学院昆明植物研究所中国西南野生生物种质资源库, 昆明 650201
2 中国科学院大学昆明生命科学学院, 昆明 650201

收稿日期:2019-04-02 接受日期:2019-07-07 出版日期:2019-11-20 发布日期:2019-11-20
通讯作者: 卢金梅
基金资助:
中国科学院重大科技基础设施开放研究项目(2017-LSF-GBOWS-02);云南省科技领军人才培养计划(2017HA014)

Advances in the evolution of plastid genome structure in lycophytes and ferns

Xinyu Du^1,²,Jinmei Lu^1,^*(),Dezhu Li^1,²

1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201
2 Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming 650201

Received:2019-04-02 Accepted:2019-07-07 Online:2019-11-20 Published:2019-11-20
Contact: Lu Jinmei

摘要/Abstract

摘要：

近年来, 随着测序技术的发展, 石松类和蕨类植物的核基因组、质体基因组以及线粒体基因组研究发展迅速, 质体基因组研究工作更是呈爆发式增长。截至2019年3月1日, GenBank公布的石松类和蕨类植物的175个质体基因组中, 约3/4为最近两年新增。研究内容从早期对个别质体基因组结构和序列特征的简单报道, 逐渐发展到综合性的比较基因组学和系统发育基因组学研究。目前已发表的质体基因组覆盖了石松类和蕨类植物的所有目和大部分科, 这两大类群的质体基因组结构变异和系统发育的基本框架已逐渐清晰。这些研究为我们理解维管植物的早期演化提供了重要参考。本文对石松类和蕨类植物的质体基因组结构特征进行了系统梳理, 发现其结构变异主要包括大片段倒位、IR区边界变动、基因或内含子丢失等, 其中一些结构变异可作为较高分类阶元的共衍征。RNA编辑和长片段非编码序列插入普遍存在于石松类和蕨类植物的质体基因组中, 但其起源、演化机制和功能等仍不清楚。我们对质体基因组的应用、系统发育研究中质体和核基因组的优劣性, 以及系统发育基因组学的前景进行了评述。

关键词: 石松类, 蕨类, 质体基因组, 基因组结构变异, RNA编辑, 长片段非编码序列插入, 系统发育基因组学

Abstract

Lycophyte and fern genetic research has accumulated over recent years due to sequencing technology advancement, making nuclear, plastid, and mitochondrial genomes accessible. While early plastid genome research focused on reporting genome structures and sequence characteristics, our current understanding spans comprehensively over structural evolution and phylogenomic analyses. These studies provide us with important insight for understanding the early evolution of vascular plants. Although lycophyte and fern plastid genomes are relatively well understood, this paper summarizes the current understanding of lycophyte and fern plastid genome structure and its variation. Such variation includes large inversions, boundary shifts of repeat regions, gene and intron loss, and some of which could be recognized as synapomorphies of higher taxonomic ranks. We also review RNA editing and long noncoding sequence inserts in plastid genomes, which are prevalent in lycophytes and ferns. However, the origin, mechanism and function of such remain unclear. We also comment on the application, merit and future of plastid phylogenomics.

Key words: lycophytes, ferns, plastid genome, genome structure variation, RNA editing, long noncoding sequence insertion, phylogenomics

杜新宇, 卢金梅, 李德铢 (2019) 石松类和蕨类植物质体基因组结构演化研究进展. 生物多样性, 27, 1172-1183. DOI: 10.17520/biods.2019113.

Xinyu Du, Jinmei Lu, Dezhu Li (2019) Advances in the evolution of plastid genome structure in lycophytes and ferns. Biodiversity Science, 27, 1172-1183. DOI: 10.17520/biods.2019113.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019113

https://www.biodiversity-science.net/CN/Y2019/V27/I11/1172

图/表 2

图1 石松类和蕨类植物质体、线粒体和核基因组已发表情况。以科为单位统计,用柱状图和数字标注在系统树右侧。系统树基于 PPG I (2016)修改。

Fig. 1 The number of published plastid, mitochondrial and nuclear genomes for lycophytes and ferns. The numbers were measured in families and were indicated to the right of the phylogenetic tree with histograms and numbers. The phylogenetic tree is modified from PPG I (2016).

图2 石松类和蕨类植物科级水平质体基因组平均GC含量统计

Fig. 2 Average GC content of plastomes within lycophytes and ferns on the familial level

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石松类和蕨类植物质体基因组结构演化研究进展

Advances in the evolution of plastid genome structure in lycophytes and ferns

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