生物多样性 ›› 2013, Vol. 21 ›› Issue (5): 616-627.doi: 10.3724/SP.J.1003.2013.12059

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生物DNA条形码: 十年发展历程、研究尺度和功能

裴男才*(), 陈步峰   

  1. 中国林业科学研究院热带林业研究所, 国家林业局珠江三角洲森林生态系统定位研究站, 广州 510520
  • 收稿日期:2013-03-07 接受日期:2013-09-04 出版日期:2013-09-20
  • 通讯作者: 裴男才 E-mail:nancai.pei@gmail.com
  • 基金项目:
    国家自然科学基金(31200471);中国林科院热林所基本科研业务费专项资金项目(RITFYWZX201208);“十二五”农村领域国家科技计划(2011BAD38B0305)

DNA barcoding of life: a classification of uses according to function and scale after ten years of development

Nancai Pei*(), Bufeng Chen   

  1. Forest Ecosystem Station of the Pearl River Delta, State Forestry Administration, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520
  • Received:2013-03-07 Accepted:2013-09-04 Online:2013-09-20
  • Contact: Pei Nancai E-mail:nancai.pei@gmail.com

DNA条形码为现代生物学研究提供了丰富的分子信息、标准的数据平台和通用的技术规程。本文从动物、植物和微生物等三方面简要梳理了生物DNA条形码近十年来的兴起和发展历程。参照DNA条形码特征, 将其生物学功能归纳为基本功能(如储备数据、鉴别物种)、延伸功能(如构建系统发育关系、服务特定行业、编制新一代生物图志)以及潜在功能(如物种整合)等三类。根据研究尺度, 划分出类群(主要是专科专属类研究)、群落(以自然保护区和大型固定样地构成的生物群落)和区域(生物多样性热点地区)等三个水平。列出了国际生命条形码组织开展的十大类研究项目, 从系统与分类学、生物多样性保护、系统发育进化生态学和数字化平台建设等四个方面分析了DNA条形码方法涉及的若干重要科学议题, 并指出在各学科应用时可能遇到的问题。DNA条形码技术在生物科学领域潜力巨大, 但还需在研究和论证过程中不断完善。

关键词: 条形码技术, 生物资源, 生物多样性保护, 生物信息数字平台, 现代生物学

DNA barcoding technology provides molecular information, standard dataset platforms, and universal technical regulations for modern biological research. We briefly review the history of DNA barcoding between 2003 and 2012, and classify DNA barcoding into three types of biological function: basic function (e.g., storing data, and identifying species), extending function (e.g., building phylogenies, serving specific subjects, and compiling biological atlas) and potential function (e.g., revealing cryptic species). We sort DNA barcoding studies at three levels: clade scale (e.g., familial and/or generic taxa), community scale (e.g., biotic communities in nature reserves and permanent forest dynamics plots), and regional scale (e.g., biodiversity hotpots). We further list ten major research programs proposed by the International Barcode of Life, which are related to DNA barcoding approaches from the prospective of systematics and taxonomy, biodiversity conservation, evolutionary ecology and phylogenetics, and the construction of digital platforms. We appreciate the huge capability of barcoding technology in the field of biological sciences, and also realize the challenges of DNA barcoding utilizations in multidisciplinary studies and the essential to add more tests before the large-scale applications.

Key words: barcoding technology, biological resource, biodiversity conservation, bioinformation digital platform, modern biology

表1

常用生物DNA条形码片段一览表"

类别
Item
片段名称
Barcode
引物
Primer sequence (5′- 3′)
来源
Source
序列长度
Size (bp)
参考文献
References
动物
Animal
COI 正向: GGTCAACAAATCATAAAGATATTGG
反向: TAAACTTCAGGGTGACCAAAAAATCA
线粒体基因编码区
Coding region in mitochondrial gene
~650 Hebert et al., 2003a
植物
Plant
rbcL



matK





trnH-psbA


ITS



trnL-F




rps4
正向: ATGTCACCACAAACAGAGACTAAAGC
反向: GTYAAATCAAGTCCACCYCG


正向: CGTACAGTACTTTTGTGTTTACGAG
反向: ACCCAGTCCATCTGGAAATCTTGGTTC
matK472F: CCCRTYCATCTGGAAATCTTGGTTC
matK1248R: GCTRTRATAATGAGAAAGATTTCTGC


trnH端: CGCGCATGGTGGATTCACAATCC
psbA端: GTTATGCATGAACGTAATGCTC

正向: AGAAGTCGTAACAAGGTTTCCGTAGG
反向: TCCTCCGCTTATTGATATGC


正向: AGAAGTCGTAACAAGGTTTCCGTAGG或GGAAGGAGAAGTCGTAACAAGG;
(裸子植物正向: GTCCACTGAACCTTATCATTTAG)
反向: TCCTCCGCTTATTGATATGC

GTAAAACGACGGCCAGT
CA-GGAA-ACAGCTATGAC
叶绿体基因编码区
Coding region in chloroplast gene


叶绿体基因编码区
Coding region in chloroplast gene

叶绿体非编码基因间隔区
Non-coding intergenic region in chloroplast gene

核基因非编码基因间隔区
Non-coding intergenic region in nuclear gene


叶绿体非编码基因间隔区
Non-coding intergenic region in chloroplast gene

叶绿体基因编码区
Coding region in chloroplast gene
~550



~850

~776



280-750


~500(由多个较短序列组成)



350-500



700-900
CBOL Plant Working Group, 2009; Kress & Erickson, 2007


Kim KJ, unpublished primers (http://www.korea.edu/academics/01co_04.php)

Yu et al., 2011



Kress & Erickson, 2007


China Plant BOL Group, 2011




de Groot et al., 2011



Nadot et al., 1994
刘艳等, 2011
微生物
Microbe
ITS


18S rDNA
正向: TCCTCCGCTTATTGATATGC
反向: GGAAGTAAAAGTCGTAACAAGG

正向: AGATTAAGCCATGCATGTCT
反向: GATCCTTCCGCAGGTTCACCTAC
核基因非编码基因间隔区
Non-coding intergenic region in nuclear gene

核基因编码区
Coding region in nuclear gene
400-660



1,600
Seifert, 2009; Schoch et al., 2012; 张宇和郭良栋, 2012


Pawlowski et al., 2012

图1

DNA条形码的技术流程示意图(改自Janzen et al., 2009以及Paul Hebert教授于2009年在北京CBOL会议上使用的PPT)"

图2

DNA条形码研究路线图"

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