Selection of candidate coding DNA barcoding regions for use on land plants

被引：229

作者：

Ford, Caroline S. ^{[1
]}

Ayres, Karen L. ^{[2
]}

Toomey, Nicola ^{[3
]}

Haider, Nadia ^{[4
]}

Stahl, Jonathan Van Alphen ^{[5
]}

Kelly, Laura J. ^{[5
]}

Wikstrom, Niklas ^{[5
,6
]}

Hollingsworth, Peter M. ^{[7
]}

Duff, R. Joel ^{[8
]}

Hoot, Sarah B. ^{[9
]}

Cowan, Robyn S. ^{[5
]}

Chase, Mark W. ^{[5
]}

Wilkinson, Mike J. ^{[1
]}

机构：

[1] Aberystwyth Univ, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DA, Dyfed, Wales

[2] Univ Reading, Sch Biol Sci, Reading RG6 6FN, Berks, England

[3] Univ London Imperial Coll Sci Technol & Med, Dept Biol Sci, Ascot SL5 7PY, Berks, England

[4] AECS, Dept Mol Biol & Biotechnol, Damascus, Syria

[5] Royal Bot Gardens, Jodrell Lab, Richmond TW9 3DS, Surrey, England

[6] Uppsala Univ, Dept Systemat Bot, S-75236 Uppsala, Sweden

[7] Royal Bot Gardens, Edinburgh EH3 5LR, Midlothian, Scotland

[8] So Illinois Univ, Dept Plant Biol, Carbondale, IL 62901 USA

[9] Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53211 USA

来源：

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY | 2009年 / 159卷 / 01期

关键词：

genetic barcodes; matK; MT-PCR; multi-locus barcode; plant identification; plastid genes; CHLOROPLAST GENOME; IDENTIFICATION; ALGORITHMS; SEQUENCE; GENES; COX1; RBCL;

D O I：

10.1111/j.1095-8339.2008.00938.x

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

An in silico screen of 41 of the 81 coding regions of the Nicotiana plastid genome generated a shortlist of 12 candidates as DNA barcoding loci for land plants. These loci were evaluated for amplification and sequence variation against a reference set of 98 land plant taxa. The deployment of multiple primers and a modified multiplexed tandem polymerase chain reaction yielded 85-94% amplification across taxa, and mean sequence differences between sister taxa of 6.1 from 156 bases of accD to 22 from 493 bases of matK. We conclude that loci should be combined for effective diagnosis, and recommend further investigation of the following six loci: matK, rpoB, rpoC1, ndhJ, ycf5 and accD. (C) 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 1-11.

引用

页码：1 / 11

页数：11

共 37 条

[1] Evolution of mitochondrial gene content: gene loss and transfer to the nucleus [J].

Adams, KL ;

Palmer, JD .

MOLECULAR PHYLOGENETICS AND EVOLUTION, 2003, 29 (03) :380-395

[2] Signal background estimation and baseline correction algorithms for accurate DNA sequencing [J].

Andrade, L ;

Manolakos, ES .

JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 2003, 35 (03) :229-243

[3] 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

[4] Land plants and DNA barcodes: short-term and long-term goals [J].

Chase, MW ;

Salamin, N ;

Wilkinson, M ;

Dunwell, JM ;

Kesanakurthi, RP ;

Haider, N ;

Savolainen, V .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2005, 360 (1462) :1889-1895

[5] Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants [J].

Cho, Y ;

Mower, JP ;

Qiu, YL ;

Palmer, JD .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (51) :17741-17746

[6] Explosive invasion of plant mitochondria by a group I intron [J].

Cho, Y ;

Qiu, YL ;

Kuhlman, P ;

Palmer, JD .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (24) :14244-14249

[7] An assessment of potential diatom "barcode" genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta) [J].

Evans, Katharine M. ;

Wortley, Alexandra H. ;

Mann, David G. .

PROTIST, 2007, 158 (03) :349-364

[8] Base-calling of automated sequencer traces using phred.: II.: Error probabilities [J].

Ewing, B ;

Green, P .

GENOME RESEARCH, 1998, 8 (03) :186-194

[9] Barcoding generalist predators by polymerase chain reaction: carabids and spiders [J].

Greenstone, MH ;

Rowley, DL ;

Heimbach, U ;

Lundgren, JG ;

Pfannenstiel, RS ;

Rehner, SA .

MOLECULAR ECOLOGY, 2005, 14 (10) :3247-3266

[10]

HAIDER N, 2003, THESIS U READING

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