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
[1]   Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa [J].
Ahmed, Ibrar ;
Matthews, Peter J. ;
Biggs, Patrick J. ;
Naeem, Muhammad ;
McLenachan, Patricia A. ;
Lockhart, Peter J. .
MOLECULAR ECOLOGY RESOURCES, 2013, 13 (05) :929-937
[2]   Mutational Dynamics of Aroid Chloroplast Genomes [J].
Ahmed, Ibrar ;
Biggs, Patrick J. ;
Matthews, Peter J. ;
Collins, Lesley J. ;
Hendy, Michael D. ;
Lockhart, Peter J. .
GENOME BIOLOGY AND EVOLUTION, 2012, 4 (12) :1316-1323
[3]   Ribosomal ITS sequences and plant phylogenetic inference [J].
Alvarez, I ;
Wendel, JF .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2003, 29 (03) :417-434
[4]  
Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI [10.1073/pnas.0812297106, 10.1073/pnas.0905845106]
[5]   Chloroplast genome analysis of Australian eucalypts - Eucalyptus, Corymbia, Angophora, Allosyficarpia and Stockwellia (Myrtaceae) [J].
Bayly, Michael J. ;
Rigault, Philippe ;
Spokevicius, Antanas ;
Ladiges, Pauline Y. ;
Ades, Peter K. ;
Anderson, Charlotte ;
Bossinger, Gerd ;
Merchant, Andrew ;
Udovicic, Frank ;
Woodrow, Ian E. ;
Tibbits, Josquin .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2013, 69 (03) :704-716
[6]   Hybridization may facilitate in situ survival of endemic species through periods of climate change [J].
Becker, Matthias ;
Gruenheit, Nicole ;
Steel, Mike ;
Voelckel, Claudia ;
Deusch, Oliver ;
Heenan, Peter B. ;
McLenachan, Patricia A. ;
Kardailsky, Olga ;
Leigh, Jessica W. ;
Lockhart, Peter J. .
NATURE CLIMATE CHANGE, 2013, 3 (12) :1039-1043
[7]   Cryptic species as a window on diversity and conservation [J].
Bickford, David ;
Lohman, David J. ;
Sodhi, Navjot S. ;
Ng, Peter K. L. ;
Meier, Rudolf ;
Winker, Kevin ;
Ingram, Krista K. ;
Das, Indraneil .
TRENDS IN ECOLOGY & EVOLUTION, 2007, 22 (03) :148-155
[8]   The promise of a DNA taxonomy [J].
Blaxter, ML .
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2004, 359 (1444) :669-679
[9]   The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae):: Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications [J].
Chang, CC ;
Lin, HC ;
Lin, IP ;
Chow, TY ;
Chen, HH ;
Chen, WH ;
Cheng, CH ;
Lin, CY ;
Liu, SM ;
Chang, CC ;
Chaw, SM .
MOLECULAR BIOLOGY AND EVOLUTION, 2006, 23 (02) :279-291
[10]   A proposal for a standardised protocol to barcode all land plants [J].
Chase, Mark W. ;
Cowan, Robyn S. ;
Hollingsworth, Peter M. ;
van den Berg, Cassio ;
Madrinan, Santiago ;
Petersen, Gitte ;
Seberg, Ole ;
Jorgsensen, Tina ;
Cameron, Kenneth M. ;
Carine, Mark ;
Pedersen, Niklas ;
Hedderson, Terry A. J. ;
Conrad, Ferozah ;
Salazar, Gerardo A. ;
Richardson, James E. ;
Hollingsworth, Michelle L. ;
Barraclough, Timothy G. ;
Kelly, Laura ;
Wilkinson, Mike .
TAXON, 2007, 56 (02) :295-299