生物多样性 ›› 2019, Vol. 27 ›› Issue (5): 526-533.DOI: 10.17520/biods.2018209

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DNA条形码参考数据集构建和序列分析相关的新兴技术

刘山林()   

  1. 中国农业大学植物保护学院, 食品营养与人类健康高精尖创新中心, 北京 100193
  • 收稿日期:2018-07-30 接受日期:2018-12-25 出版日期:2019-05-20 发布日期:2019-05-20
  • 通讯作者: 刘山林
  • 基金资助:
    深圳市基础研究(自由探索 JCYJ20170817150755701)

DNA barcoding and emerging reference construction and data analysis technologies

Liu Shanlin()   

  1. Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193
  • Received:2018-07-30 Accepted:2018-12-25 Online:2019-05-20 Published:2019-05-20
  • Contact: Liu Shanlin

摘要:

近年来DNA条形码技术迅速发展, 产生的条形码的数量及其应用范围都呈指数性增长, 现已广泛用于物种鉴定、食性分析、生物多样性评估等方面。本文重点总结并讨论了构建条形码参考数据库和序列聚类相关的信息分析的技术和方法, 包括: 基于高通量测序(high throughput sequencing, HTS)平台以高效并较低的成本获取条形码序列的方法; 同时还介绍了从原始测序序列到分类操作单元(operational taxonomic units, OTUs)过程中的一些计算逻辑以及被广泛采用的软件和技术。这是一个较新并快速发展的领域, 我们希望本文能为读者提供一个梗概, 了解DNA条形码技术在生物多样性研究应用中的方法和手段。

关键词: DNA条形码, 可操作物种单元, 聚类, 宏基因条形码, 高通量测序

Abstract:

DNA barcoding has been growing exponentially in terms of the number of barcode generated as well as its applications, e.g. as conservation tools in: species identification for damaged specimens, diet analysis from gut content and feces, biodiversity assessment from environmental DNA (eDNA), bulk arthropod samples or invertebrate-derived DNA (iDNA). These applications often require coupling with high throughput sequencing (HTS) technologies, and when done so are referred to as metabarcoding. Here, we discuss the methods used to generate reference barcodes using cost-efficient HTS platforms, and introduce several rules-of-thumb and some widely-used tools to conduct data quality control, denoising, and Operational Taxonomic Units (OTUs) clustering. We hope this review will help readers better understand how these emerging technologies can be implemented alongside existing technologies to accelerate biodiversity assessments in an accurate and efficient way.

Key words: DNA barcoding, OTUs, clustering, metabarcoding, high throughput sequencing