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基因组时代的植物系统发育研究进展

王杰 贺文闯 向坤莉 武志强 顾翠花

王杰, 贺文闯, 向坤莉, 武志强, 顾翠花. 基因组时代的植物系统发育研究进展[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20220313
引用本文: 王杰, 贺文闯, 向坤莉, 武志强, 顾翠花. 基因组时代的植物系统发育研究进展[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20220313
WANG Jie, HE Wenchuang, XIANG Kunli, WU Zhiqiang, GU Cuihua. Advances in plant phylogeny in the genome era[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20220313
Citation: WANG Jie, HE Wenchuang, XIANG Kunli, WU Zhiqiang, GU Cuihua. Advances in plant phylogeny in the genome era[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20220313

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基因组时代的植物系统发育研究进展

doi: 10.11833/j.issn.2095-0756.20220313
基金项目: 浙江省自然科学基金资助项目(LY21C160001);浙江省农业新品种选育重大科技专项(2021CO2071-4)
详细信息
    作者简介: 王杰(ORCID: 0000-0003-0038-1045),从事园林植物遗传育种与系统发育研究。E-mail: wangjie@stu.zafu.edu.cn
    通信作者: 顾翠花(ORCID: 0000-0003-4086-8587),教授,博士,从事园林植物遗传育种与种质资源创新研究。E-mail: gucuihua@zafu.edu.cn
  • 中图分类号: Q941

Advances in plant phylogeny in the genome era

  • 摘要: 系统发育研究是进化生物中的基本问题,也是其他众多生物学分支学科的基础问题,其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降,系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果,总结了植物不同基因组的特征及其在系统发育研究中的优势与局限,探讨了系统发育树构建的主要方法,并对未来研究进行了展望。目前,植物体内的3套基因组适用于不同阶元和类群的系统发育研究,不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用:① 叶绿体基因组结构相对简单,序列保守,不易重组,单亲遗传,是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源;②植物线粒体基因组序列进化速率较慢,目前仅适用于早期植物和大尺度水平的系统发育研究;③核基因组为双亲遗传,可综合揭示双亲谱系及系统网状进化关系,在系统发育研究中具有巨大的应用潜力。不同建树方法适用于不同特征的数据集,在建树过程中应采用合理的方法避免长枝吸引和不完全谱系分选带来的影响。未来核基因组将成为系统发育研究的主流方向,其双亲遗传特性能够为物种形成过程中的杂交和基因组渗入等事件提供充分的见解。随着越来越多的类群系统位置被确定,物种形成和进化过程中的杂交、回交等双亲遗传,以及核质互作、多倍化、功能适应和趋同进化等问题将会成为系统发育研究的重点。表1参78
  • 表  1  基于不同基因组数据集的植物系统发育相关研究

    Table  1.   Research on phylogenetics of plants based on various genome datasets

    研究对象数据集参考文献
    绿色植物 1 879种物种的完整或近完整cpDNA [13]
    被子植物 2 881种物种的80个叶绿体基因编码序列 [14]
    被子植物 开花植物目前所有科下2 024属4 660种物种的80条叶绿体基因编码序列 [10]
    鸭跖草类 46种non-Poalean鸭跖草类物种的83个叶绿体基因编码序列 [15]
    胡桃科Juglandaceae 17种物种的RAD-Seq、19种物种的完整cpDNA [16]
    禾本科Poaceae 127种禾本科物种的完整cpDNA [17]
    西番莲属Passiflora 49种物种的68个叶绿体基因编码序列 [18]
    长冠菀属Diplostephium 74种长冠菀属物种的核核糖体顺反子序列、完整cpDNA、部分线粒体基因编码序列、
     双酶切简化基因组(double digest-RAD,dd-RAD)
    [19]
    被子植物 91种物种的38个线粒体基因编码序列 [20]
    苔藓植物 60种物种的41个线粒体基因编码序列 [21]
    被子植物 151种物种转录组筛选的1594个核基因编码序列 [22]
    被子植物 119种物种转录组筛选的665个低拷贝核基因编码序列 [23]
    禾本科基部类群 14种禾本科物种基因组筛选的480个低拷贝核基因编码序列 [24]
    昆栏树目Trochodendrales 19种物种基因组筛选的214 个单拷贝核基因编码序列 [25]
    十字花科Brassicaceae 32种物种转录组筛选的113个低拷贝核编码基因 [26]
    蔷薇科Rosaceae 124种物种转录组筛选的882个低拷贝核编码基因序列 [27]
    下载: 导出CSV
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  • 收稿日期:  2022-04-23
  • 录用日期:  2022-08-14
  • 修回日期:  2022-08-10

基因组时代的植物系统发育研究进展

doi: 10.11833/j.issn.2095-0756.20220313
    基金项目:  浙江省自然科学基金资助项目(LY21C160001);浙江省农业新品种选育重大科技专项(2021CO2071-4)
    作者简介:

    王杰(ORCID: 0000-0003-0038-1045),从事园林植物遗传育种与系统发育研究。E-mail: wangjie@stu.zafu.edu.cn

    通信作者: 顾翠花(ORCID: 0000-0003-4086-8587),教授,博士,从事园林植物遗传育种与种质资源创新研究。E-mail: gucuihua@zafu.edu.cn
  • 中图分类号: Q941

摘要: 系统发育研究是进化生物中的基本问题,也是其他众多生物学分支学科的基础问题,其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降,系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果,总结了植物不同基因组的特征及其在系统发育研究中的优势与局限,探讨了系统发育树构建的主要方法,并对未来研究进行了展望。目前,植物体内的3套基因组适用于不同阶元和类群的系统发育研究,不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用:① 叶绿体基因组结构相对简单,序列保守,不易重组,单亲遗传,是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源;②植物线粒体基因组序列进化速率较慢,目前仅适用于早期植物和大尺度水平的系统发育研究;③核基因组为双亲遗传,可综合揭示双亲谱系及系统网状进化关系,在系统发育研究中具有巨大的应用潜力。不同建树方法适用于不同特征的数据集,在建树过程中应采用合理的方法避免长枝吸引和不完全谱系分选带来的影响。未来核基因组将成为系统发育研究的主流方向,其双亲遗传特性能够为物种形成过程中的杂交和基因组渗入等事件提供充分的见解。随着越来越多的类群系统位置被确定,物种形成和进化过程中的杂交、回交等双亲遗传,以及核质互作、多倍化、功能适应和趋同进化等问题将会成为系统发育研究的重点。表1参78

English Abstract

王杰, 贺文闯, 向坤莉, 武志强, 顾翠花. 基因组时代的植物系统发育研究进展[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20220313
引用本文: 王杰, 贺文闯, 向坤莉, 武志强, 顾翠花. 基因组时代的植物系统发育研究进展[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20220313
WANG Jie, HE Wenchuang, XIANG Kunli, WU Zhiqiang, GU Cuihua. Advances in plant phylogeny in the genome era[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20220313
Citation: WANG Jie, HE Wenchuang, XIANG Kunli, WU Zhiqiang, GU Cuihua. Advances in plant phylogeny in the genome era[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20220313

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