生物多样性

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石松类和蕨类植物质体基因组研究进展(蕨类植物多样性专辑)

杜新宇1, 2, 卢金梅2, 李德铢2   

  1. 1. 中国科学院大学昆明生命科学学院
    2. 中国科学院昆明植物研究所
  • 收稿日期:2019-04-02 修回日期:2019-07-17 出版日期:2019-10-22
  • 通讯作者: 卢金梅

Advances in research of plastid genomes in lycophytes and ferns

Xinyu Du1, 2, Jinmei Lu2, Dezhu Li2   

  1. 1. Kunming College of Life Sciences, University of Chinese Academy of Sciences
    2. Kunming Institute of Botany, Chinese Academy of Sciences
  • Received:2019-04-02 Revised:2019-07-17 Online:2019-10-22
  • Contact: Jinmei Lu

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,截止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。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

In very recent years, there has been an exponential increase in the number of genomes (including nuclear, plastid and mitochondria genomes) for the lycophytes and ferns, due primarily to developments in sequencing technologies. Of the 175 plastid genomes available on GenBank (last accessed on March 1, 2019), about three quarters were published during the past two years. Early plastid genome research focused mainly on simply reporting individual structures and sequence characteristics, while later developed into comprehensive structural evolution and phylogenomic analyses. The plastid genomes currently released have covered all orders and most families of lycophytes and ferns, and the general framework of variation in plastid genome structure and phylogeny have become gradually clearer. In this paper, we summarize researches on structural variation of plastid genome within lycophytes and ferns, and show that this variation mainly includes large inversions, boundary shifts of the repeat regions, and loss of genes or introns, and some of which could be recognized as synapomorphies of higher taxonomic ranks. Additionally, we briefly review research of RNA editing and long noncoding sequence insertion in plastid genomes within lycophytes and ferns. These phenomena are prevalent in plastid genomes, but their origin, evolution mechanism and function are still unclear. We also comment on the applications of plastid genomes, the merit of using plastid and nuclear genomes in phylogenetic research, as well as the future of phylogenomics.

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

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