Selection of candidate coding DNA barcoding regions for use on land plants
C. S. Ford(Institute of Biological, Environmental and Rural Sciences), Karen L. Ayres(University of Reading), Nicola H. Toomey(Imperial College London), Nadia Haider(Atomic Energy Commission of Syria), JONATHAN VAN ALPHEN STAHL(Royal Botanic Gardens, Kew), Laura J. Kelly(Royal Botanic Gardens, Kew), Niklas Wikström(Uppsala University), Peter M. Hollingsworth(Royal Botanic Garden Edinburgh), R. Joel Duff(Southern Illinois University Carbondale), SARAH B. HOOT(University of Wisconsin–Milwaukee), Robyn S. Cowan(Royal Botanic Gardens, Kew), Mark W. Chase(Royal Botanic Gardens, Kew), M. J. Wilkinson(Institute of Biological, Environmental and Rural Sciences)
Cited by 315Open Access
Abstract
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.
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