Plant DNA barcoding: from gene to genome

被引:605
作者
Li, Xiwen [1 ]
Yang, Yang [1 ]
Henry, Robert J. [2 ]
Rossetto, Maurizio [3 ,4 ]
Wang, Yitao [1 ]
Chen, Shilin [5 ]
机构
[1] Univ Macau, State Key Lab Qual Res Chinese Med, Inst Chinese Med Sci, Macau 999078, Peoples R China
[2] Univ Queensland, Queensland Alliance Agr & Food Innovat, Brisbane, Qld 4072, Australia
[3] Royal Bot Gardens, Natl Herbarium NSW, Sydney, NSW 2000, Australia
[4] Domain Trust, Sydney, NSW 2000, Australia
[5] China Acad Chinese Med Sci, Inst Chinese Mat Med, Beijing 100700, Peoples R China
关键词
single-locus barcode; universal; plastid-sequencing; super-barcode; specific barcode; COMPLETE CHLOROPLAST GENOME; SPECIES IDENTIFICATION; PLASTID GENOME; LAND PLANTS; ORDER PHYLOGENY; SEQUENCES; MARKERS; RBCL; HYBRIDIZATION; POPULATION;
D O I
10.1111/brv.12104
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species. Because single-locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole-chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies. While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource-effective and does not yet offer the speed of analysis provided by single-locus barcodes to unspecialized laboratory facilities. Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super-barcode. We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single-locus barcodes and super-barcodes for efficient plant identification. Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels.
引用
收藏
页码:157 / 166
页数:10
相关论文
共 100 条
[41]   JML: testing hybridization from species trees [J].
Joly, Simon .
MOLECULAR ECOLOGY RESOURCES, 2012, 12 (01) :179-184
[42]   A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting [J].
Joly, Simon ;
McLenachan, Patricia A. ;
Lockhart, Peter J. .
AMERICAN NATURALIST, 2009, 174 (02) :E54-E70
[43]   ULTRA-BARCODING IN CACAO (THEOBROMA SPP.; MALVACEAE) USING WHOLE CHLOROPLAST GENOMES AND NUCLEAR RIBOSOMAL DNA [J].
Kane, Nolan ;
Sveinsson, Saemundur ;
Dempewolf, Hannes ;
Yang, Ji Yong ;
Zhang, Dapeng ;
Engels, Johannes M. M. ;
Cronk, Quentin .
AMERICAN JOURNAL OF BOTANY, 2012, 99 (02) :320-329
[44]   Botany without borders: barcoding in focus [J].
Kane, Nolan C. ;
Cronk, Quentin .
MOLECULAR ECOLOGY, 2008, 17 (24) :5175-5176
[45]   A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region [J].
Kress, W. John ;
Erickson, David L. .
PLOS ONE, 2007, 2 (06)
[46]   Use of DNA barcodes to identify flowering plants [J].
Kress, WJ ;
Wurdack, KJ ;
Zimmer, EA ;
Weigt, LA ;
Janzen, DH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (23) :8369-8374
[47]  
Kuang DY, 2011, GENOME, V54, P663, DOI [10.1139/G11-026, 10.1139/g11-026]
[48]   Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines [J].
Kumar, Shashi ;
Hahn, Frederick M. ;
McMahan, Colleen M. ;
Cornish, Katrina ;
Whalen, Maureen C. .
BMC PLANT BIOLOGY, 2009, 9
[49]   DNA barcoding the floras of biodiversity hotspots [J].
Lahaye, Renaud ;
Van der Bank, Michelle ;
Bogarin, Diego ;
Warner, Jorge ;
Pupulin, Franco ;
Gigot, Guillaume ;
Maurin, Olivier ;
Duthoit, Sylvie ;
Barraclough, Timothy G. ;
Savolainen, Vincent .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (08) :2923-2928
[50]   Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants [J].
Li, De-Zhu ;
Gao, Lian-Ming ;
Li, Hong-Tao ;
Wang, Hong ;
Ge, Xue-Jun ;
Liu, Jian-Quan ;
Chen, Zhi-Duan ;
Zhou, Shi-Liang ;
Chen, Shi-Lin ;
Yang, Jun-Bo ;
Fu, Cheng-Xin ;
Zeng, Chun-Xia ;
Yan, Hai-Fei ;
Zhu, Ying-Jie ;
Sun, Yong-Shuai ;
Chen, Si-Yun ;
Zhao, Lei ;
Wang, Kun ;
Yang, Tuo ;
Duan, Guang-Wen .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (49) :19641-19646