利用标本组学推进植物超级DNA条形码研究

doi:10.11983/CBB22194

植物学报 ›› 2023, Vol. 58 ›› Issue (5): 831-842.DOI: 10.11983/CBB22194

• 专题论坛 • 上一篇

利用标本组学推进植物超级DNA条形码研究

王露露¹^,²^,³, 杨智¹^,²^,³, 杨永¹^,²^,³^,^*()

1.南京林业大学南方现代林业协同创新中心, 南京 210037
2.南京林业大学生命科学学院, 南京 210037
3.南京林业大学国家林业和草原局亚热带森林生物多样性保护重点实验室, 南京 210037

收稿日期:2022-08-12 接受日期:2023-02-09 出版日期:2023-09-01 发布日期:2023-09-21
通讯作者: *E-mail: yangyong@njfu.edu.cn
基金资助:
江苏省自然科学基金(BK202-11279);国家自然科学基金(31970205);南京林业大学水杉英才项目

Plant Ultra-barcoding Using Herbariomics

Wang Lulu¹^,²^,³, Yang Zhi¹^,²^,³, Yang Yong¹^,²^,³^,^*()

1. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2. College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
3. Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China

Received:2022-08-12 Accepted:2023-02-09 Online:2023-09-01 Published:2023-09-21
Contact: *E-mail: yangyong@njfu.edu.cn

摘要/Abstract

摘要： 物种的准确鉴定是生物资源利用和物种保护的重要基础。传统的物种鉴定依赖于分类学专业人员, 而培养分类学专业人员需要耗费大量时间, 是分类学知识利用的瓶颈。利用多通道电子检索表和智能识别也因个体发育阶段的不同和形态变异而难以准确鉴定物种。DNA条形码是基于DNA序列的鉴定技术, 不受个体发育和形态多态性的影响, 为物种快速鉴定提供了有效的解决方案。该文综述了DNA条形码的类型和发展趋势。DNA条形码的发展历史可分为2个阶段: (1) 以一代测序为序列获取方式的单片段或少量片段时期; (2) 以新一代高通量测序为序列获取方式的超级DNA条形码时期。该文比较了2个发展阶段DNA条形码的主要特点、研究方法和物种鉴定能力, 认为基于质体基因组的超级DNA条形码物种鉴定能力更强, 发展超级DNA条形码将成为植物条形码研究的主要趋势。同时进一步总结了超级DNA条形码发展所面临的困境和解决思路, 指出研究材料仍是当前限制超级DNA条形码发展的关键因素, 提出利用标本组学方法捕获大量历史馆藏标本的基因组序列, 可为开展超级DNA条形码研究提供省时、高效和经济的解决方案。通过挖掘植物基因组数据获得单拷贝和低拷贝核基因并应用于物种条形码研究, 不仅能提升分辨率, 而且可解决杂交和不完全谱系分选等复杂进化历史类群的分类问题。建议利用标本馆保存的珍贵标本资源建立植物超级DNA条形码参考序列数据库。

关键词: 标本组学, 鉴定, 物种, 分类学, 超级DNA条形码

Abstract: Both biological conservation practices and utilization of biological resources need accurate identification. Traditional species identification relies on taxonomic specialists, but the training of taxonomic specialists is time-consuming, which leads to a bottleneck in the utilization of taxonomic knowledge. Interactive keys and Apps based on artificial intelligence are often unable to accurately identify species because of developmental stage differences and morphological variation. DNA barcoding is an effective identification technique, its identification results based on DNA sequences are not dependent upon developmental stages and morphological polymorphism, which makes it an ideal solution to rapid species identification. Here we reviewed the types and development trends of DNA barcoding. The development of DNA barcoding can be divided into two main phases: (1) The initial phase of a single marker or combination of a few markers based on the Sanger-sequencing method; (2) The ultra-barcoding phase based on the Next-generation sequencing method. We compared the main characteristics, research methods, and species identification power of different DNA barcoding methods in these two development phases. In general, the ultra-barcoding based on plastomes performs better in species identification than normal barcodes of the first phase, and is likely to become the main method of DNA barcode research. This review summarized the difficulties and solutions of DNA barcoding development. Research material availability remains the key limitation for developing ultra-barcodes of plants. Herbariomics can capture genomic data from herbarium specimens and is thus a time-saving, highly efficient and economical approach for ultra-barcoding studies. Botanists can also obtain single-copy or low-copy nuclear genes by mining herbariomic data, and thus can apply the nuclear genes in barcoding analyses to improve the species discrimination resolution and resolve the identification problems of those plant groups with complicated evolutionary history including incomplete lineage sorting and hybridization. We thus propose to mine the treasures of herbarium specimens and establish the reference database of ultra-barcoding.

Key words: herbariomics, identification, species, taxonomy, ultra-barcoding

王露露, 杨智, 杨永. 利用标本组学推进植物超级DNA条形码研究. 植物学报, 2023, 58(5): 831-842.

Wang Lulu, Yang Zhi, Yang Yong. Plant Ultra-barcoding Using Herbariomics. Chinese Bulletin of Botany, 2023, 58(5): 831-842.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22194

https://www.chinbullbotany.com/CN/Y2023/V58/I5/831

图/表 2

图1 Web of Science数据库历年发表的DNA条形码论文统计 (A) 2003-2022年DNA条形码相关文章数量; (B) 不同学科研究方向DNA条形码相关文章数量

Figure 1 Publications of DNA barcodes in the Web of Science database over years (A) Number of articles related to DNA barcoding published in 2003-2022; (B) Number of articles related to DNA barcoding published in different disciplines

表1 5种常用基因组划分方法的比较

Table 1 Comparison of five commonly used methods for genome partitioning

测序技术	实验成本	最终成本	DNA质量要求	同源序列的识别能力	生物信息学专门知识	是否适用于标本材料
简化基因组测序	高	低	中-高	难	中级/高级	否
转录组测序	低	低	中-高	相对容易	中级	否
杂交捕获测序	低	中	低-中	容易	中级/高级	是
扩增子测序	低	中	低-中	容易	初级	是
基因组浅层测序	低	中	低-中	容易	初级	是

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利用标本组学推进植物超级DNA条形码研究

Plant Ultra-barcoding Using Herbariomics

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