生物DNA条形码: 十年发展历程、研究尺度和功能

doi:10.3724/SP.J.1003.2013.12059

摘要/Abstract

摘要：

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

Abstract

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

裴男才, 陈步峰 (2013) 生物DNA条形码: 十年发展历程、研究尺度和功能. 生物多样性, 21, 616-627. DOI: 10.3724/SP.J.1003.2013.12059.

Nancai Pei,Bufeng Chen (2013) DNA barcoding of life: a classification of uses according to function and scale after ten years of development. Biodiversity Science, 21, 616-627. DOI: 10.3724/SP.J.1003.2013.12059.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2013.12059

https://www.biodiversity-science.net/CN/Y2013/V21/I5/616

图/表 3

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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

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

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