标本组学——树木学研究的新方法

doi:10.12302/j.issn.1000-2006.202104022

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (1): 1-6.doi: 10.12302/j.issn.1000-2006.202104022

标本组学——树木学研究的新方法

杨永(), 杨智(), 段一凡, 方炎明

南京林业大学生物与环境学院,江苏南京 210037

收稿日期:2021-04-15 接受日期:2021-06-28 出版日期:2022-01-30 发布日期:2022-02-09
基金资助:
国家自然科学基金项目(31970205);国家自然科学基金项目(31770211);江苏省自然科学基金项目(BK20211279);南京林业大学水杉英才项目

Herbariomics: a new and powerful approach for dendrological studies

YANG Yong(), YANG Zhi(), DUAN Yifan, FANG Yanming

College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China

Received:2021-04-15 Accepted:2021-06-28 Online:2022-01-30 Published:2022-02-09

摘要/Abstract

摘要：

树木学是一门不断发展、高度综合的学科。系统发生是树木学的基础,研究材料和序列数据一直是限制系统发生重建的重要因素。新技术的发展和应用通过拓展材料利用、改进和提升系统发生树的分辨率而将树木学的研究推向新的高度。标本馆不仅是树木物种凭证标本的保存地,保存了物种的形态、地理分布、生态、物候等信息,而且是重要的材料库。标本材料因制作和保存过程中高温和氧化导致基因组DNA降解和破碎化,一代测序技术由于技术限制而无法充分利用馆藏标本开展生命之树重建研究。新兴的标本组学是近年来基于二代测序技术发展起来的获取标本材料中基因组DNA的技术,这种技术通过对短片段测序和生物信息学方法拼接获得基因组DNA序列,因此可以充分利用馆藏标本材料,结合浅层测序和靶序列捕获能获得包括nrITS、叶绿体基因组、线粒体基因组以及单拷贝核基因等序列,从而满足系统发生重建的需要,且有着经济、省时、高效、准确的优势。新兴标本组学的应用将加速生命之树重建、DNA条形码、物种保护和资源可持续利用等方面的研究。

关键词: 树木分类, 标本组学, 系统发生

Abstract:

Dendrology is a branch of biology, dealing with the characteristics of woody plants; and phylogeny is the basis of dendrology. Common limiting factors in phylogenetic studies include inadequate species sampling and the availability of sufficient sequence data. The application of new approaches may broaden the range of materials to be utilized and thereby improve the resolution of phylogenies, thus advancing dendrological studies to higher levels. Herbaria preserve specimens that are the permanent vouchers for species; they comprise an important resource bank, storing information on morphology, distribution, ecology and phenology, and also plant materials. Herbarium specimens contain deoxyribonucleic acid (DNA) sequences fragmented due to degradation and oxidization during specimen preparation and preservation. As such, Sanger sequencing cannot make full use of herbarium specimens in phylogenetic studies due to these limitations. This study introduces a novel method referred to as herbariomics, in which DNA sequences (i.e., nrITS, plastomes, mitomes and single-copy nuclear genes) can be obtained from herbarium specimens by using next-generation sequencing and bioinformatics methodologie. Herbariomics enable low-cost, time-saving, highly efficient, and accurate dendrological research. Its application is likely to accelerate research associated with reconstructing the Tree of Life, DNA barcoding, species conservation, and the sustainable utilization of trees.

Key words: dendrology and taxonomy, herbariomics, phylogeny

中图分类号:

S718.4

杨永,杨智,段一凡,等. 标本组学——树木学研究的新方法[J]. 南京林业大学学报（自然科学版）, 2022, 46(1): 1-6.

YANG Yong, YANG Zhi, DUAN Yifan, FANG Yanming. Herbariomics: a new and powerful approach for dendrological studies[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(1): 1-6.DOI: 10.12302/j.issn.1000-2006.202104022.

图/表 2

表1

标本组学与一代测序、扩增子测序、浅层测序、转录组测序、简化基因组和靶序列捕获技术的比较(修改自Yu等[36])"

技术 technique	材料要求 material requirements	DNA质量要求 DNA quality requirements	测序方法 sequencing method	测序对象 sequencing object	引物或探针设计 primer or probe design	获得数据 get data	同源性确定 homology determination	测序成本 sequencing cost	适用分类等级 applicable classification level
标本组学 herbariomics	要求较低,标本材料	较低	二代测序	全基因组或探针捕获位点	不需要	叶绿体基因组、线粒体基因组、nrDNA、核基因组的大多数位点	容易	较低	各个等级
一代测序 sanger sequencing	新鲜材料、硅胶干燥材料	适中	一代测序	目标序列片段	引物设计	nrITS、rbcL、psbA-trnH、matK、LEAFY等常规片段	容易	较低	各个等级
扩增子测序 amplicon sequencing	新鲜材料、硅胶干燥材料	适中	一代测序	目标序列片段	引物设计	确定的目标片段	容易	适中	各个等级
浅层测序 genome skimming	要求较低,标本、硅胶干燥材料、新鲜材料等	较低	二代测序	全基因组	不需要	叶绿体基因组、线粒体基因组、nrDNA、基因的编码区和非编码区	容易	较低	各个等级
靶序列捕获 targeted sequence capture	要求较低,标本、硅胶干燥材料、新鲜材料等	较低	二代测序	探针捕获位点	探针设计	核基因、叶绿体、线粒体,编码区和非编码区	容易	较低	各个等级
转录组测序 transcriptome	要求严格,新鲜材料	较高	二代测序	cDNA	不需要	核基因组的大多数位点,编码基因	相对容易	较高	属以上等级
简化基因组 genotyping-by- sequencing	要求较高,硅胶干燥材料、新鲜材料	适中	二代测序	限制性片段	不需要	主要是来自核基因组的SNP位点,编码区和非编码区	较难	适中	近缘属、近缘种或群体水平

表1

图1

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标本组学——树木学研究的新方法

Herbariomics: a new and powerful approach for dendrological studies

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