Use of DNA barcodes to identify flowering plants
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TLDR
Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.Abstract:
Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.read more
Citations
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Journal ArticleDOI
A DNA barcode for land plants.
Peter M. Hollingsworth,Laura L. Forrest,John L. Spouge,Mehrdad Hajibabaei,Sujeevan Ratnasingham,Michelle van der Bank,Mark W. Chase,Robyn S. Cowan,David L. Erickson,Aron J. Fazekas,Sean W. Graham,Karen E. James,Ki Joong Kim,W. John Kress,Harald Schneider,Jonathan van Alphen-Stahl,Spencer C. H. Barrett,Cássio van den Berg,Diego Bogarín,Kevin S. Burgess,Kevin S. Burgess,Kenneth M. Cameron,Kenneth M. Cameron,Mark A. Carine,Juliana Chacón,Alexandra Clark,James J. Clarkson,Ferozah Conrad,Dion S. Devey,Caroline S. Ford,Terry A. Hedderson,Michelle L. Hollingsworth,Brian C. Husband,Laura J. Kelly,Laura J. Kelly,Prasad Kesanakurti,Jung Sung Kim,Young-Dong Kim,Renaud Lahaye,Hae-Lim Lee,David G. Long,Santiago Madriñán,Olivier Maurin,Isabelle Meusnier,Steven G. Newmaster,Chong-Wook Park,Diana M. Percy,Gitte Petersen,James E. Richardson,Gerardo A. Salazar,Vincent Savolainen,Vincent Savolainen,Ole Seberg,Mike J. Wilkinson,Dong-Keun Yi,Damon P. Little +55 more
TL;DR: The 2-locus combination of rbcL+matK will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
Journal ArticleDOI
Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III
TL;DR: Nine newly explored regions of the chloroplast genome offer levels of variation better than the best regions identified in an earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.
Journal ArticleDOI
Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.
Shilin Chen,Hui Yao,Jianping Han,Chang Liu,Jingyuan Song,Linchun Shi,Yingjie Zhu,Xinye Ma,Ting Gao,Xiaohui Pang,Kun Luo,Ying Li,Xiwen Li,Xiaocheng Jia,Yulin Lin,Christine Leon +15 more
TL;DR: The second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications and can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species.
Journal ArticleDOI
The promise of DNA barcoding for taxonomy.
TL;DR: Despite the potential benefits of DNA barcoding to both the practitioners and users of taxonomy, it has been controversial in some scientific circles and a few have even characterized it as being “anti-taxonomy,” arguing that its implementation will signal the death of a system 250 years in the making.
Journal ArticleDOI
A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH- psbA Spacer Region
W. John Kress,David L. Erickson +1 more
TL;DR: A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.
References
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Journal ArticleDOI
Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data.
TL;DR: The resulting trees strongly support the monophyly of the core Laurales plus Calycanthaceae and Idiospermaceae, and several morphological character state changes are congruent with the molecular tree.
Journal ArticleDOI
Shortcuts in systematics? A commentary on DNA-based taxonomy
Ole Seberg,Christopher J. Humphries,Sandy Knapp,Dennis W. Stevenson,Gitte Petersen,Nikolaj Scharff,Nils Møller Andersen +6 more
TL;DR: The primary aims of taxonomy are to name, circumscribe, describe and classify species and registration would eventually strangle systematics, as debate will be discouraged.
Journal ArticleDOI
A molecular analysis of ground sloth diet through the last glaciation
Michael Hofreiter,Hendrik N. Poinar,Spaulding Wg,Karin Bauer,Paul S. Martin,Göran Possnert,Svante Pääbo +6 more
TL;DR: Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloths could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses.
Journal ArticleDOI
Novel perspectives in wood certification and forensics: dry wood as a source of DNA
TL;DR: Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.
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A DNA barcode for land plants.
Peter M. Hollingsworth,Laura L. Forrest,John L. Spouge,Mehrdad Hajibabaei,Sujeevan Ratnasingham,Michelle van der Bank,Mark W. Chase,Robyn S. Cowan,David L. Erickson,Aron J. Fazekas,Sean W. Graham,Karen E. James,Ki Joong Kim,W. John Kress,Harald Schneider,Jonathan van Alphen-Stahl,Spencer C. H. Barrett,Cássio van den Berg,Diego Bogarín,Kevin S. Burgess,Kevin S. Burgess,Kenneth M. Cameron,Kenneth M. Cameron,Mark A. Carine,Juliana Chacón,Alexandra Clark,James J. Clarkson,Ferozah Conrad,Dion S. Devey,Caroline S. Ford,Terry A. Hedderson,Michelle L. Hollingsworth,Brian C. Husband,Laura J. Kelly,Laura J. Kelly,Prasad Kesanakurti,Jung Sung Kim,Young-Dong Kim,Renaud Lahaye,Hae-Lim Lee,David G. Long,Santiago Madriñán,Olivier Maurin,Isabelle Meusnier,Steven G. Newmaster,Chong-Wook Park,Diana M. Percy,Gitte Petersen,James E. Richardson,Gerardo A. Salazar,Vincent Savolainen,Vincent Savolainen,Ole Seberg,Mike J. Wilkinson,Dong-Keun Yi,Damon P. Little +55 more