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
The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm.
Deden Derajat Matra,Muh Agust Nur Fathoni,Muhammad Majiidu,Hanif Wicaksono,Agung Sriyono,Gunawan Gunawan,Hilda Susanti,Rismita Sari,Fitmawati Fitmawati,Iskandar Z. Siregar,Winarso Drajad Widodo,Roedhy Poerwanto +11 more
TL;DR: In this article, the authors collected M. casturi genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis.
Dissertation
Systematic and phylogeographic implications of molecular variation in the western North American roseroot, Rhodiola integrifolia (Crassulaceae)
Abstract: The roseroot genus Rhodiola is widely distributed in arctic and alpine areas of the Northern Hemisphere. It is most speciose in the high mountain ranges of central Asia. Rhodiola integrifolia occurs at high altitudes and high latitudes in western North America and northeastern Asia. During the Pleistocene glaciations the region between Asia and North America known as Beringia was ice free and acted as a glacial refugium for coldadapted taxa. I surveyed variation in a nuclear (ITS) and chloroplast (psbA-trnH spacer) DNA region in R. integrifolia and its North American relatives, R. rosea and R. rhodantha. Phylogenetic analyses based on ITS showed that (i) the western North American species R. integrifolia and R. rhodantha are distinct but closely related sister taxa; and (ii) these two species and the eastern North American R. rosea belong to separate clades within Rhodiola. Analyses of the plastid region showed that although the
Selection of chloroplast dna markers for the development of dna barcode and reconstruction of phylogeny of senecio asirensis boulos and j.r.i. wood
TL;DR: Based on nr-ITS marker, S. asirensis clearly showed its phylogenetic relationship to the other Senecio species, suggesting its endemism to Saudi Arabia.
Journal ArticleDOI
Authentication of Illicium verum using a DNA barcode psbA-trnH
TL;DR: The notion that the psbA-trnH region could distinguish I. verum from other adulterating species was supported, and the highest inter-specific divergence among the four DNA barcoding sequences was shown.
Journal ArticleDOI
Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution.
Jose D. Zúñiga,Morgan R. Gostel,Daniel G. Mulcahy,Katharine Barker,Asia Hill,Maryam Sedaghatpour,Samantha Q Vo,Vicki A. Funk,Jonathan A. Coddington +8 more
TL;DR: The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life.
References
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Biological identifications through DNA barcodes
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Journal ArticleDOI
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
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Journal ArticleDOI
The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression.
Kazuo Shinozaki,Masaru Ohme,Minoru Tanaka,Tatsuya Wakasugi,Nobuaki Hayashida,Tohru Matsubayashi,N. Zaita,J. Chunwongse,Junichi Obokata,Kazuko Yamaguchi-Shinozaki,Chikara Ohto,Keita Torazawa,B. Y. Meng,Mamoru Sugita,Hiroshi Deno,T. Kamogashira,Kyoji Yamada,Jun Kusuda,F. Takaiwa,Akira Kato,N. Tohdoh,Hiroaki Shimada,Masahiro Sugiura +22 more
TL;DR: Five sequences coding for proteins homologous to components of the respiratory‐chain NADH dehydrogenase from human mitochondria have been found and sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.
Journal ArticleDOI
Identification of Birds through DNA Barcodes
TL;DR: The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species, and implies that a standard screening threshold of sequence difference could speed the discovery of new animal species.
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