Assessing the potential of candidate DNA barcodes for identifying non‐flowering seed plants

Pang, Xiaohui; Luo, Hui-ming; Sun, Chao

doi:10.1111/j.1438-8677.2011.00554.x

Cited by 18 publications

(11 citation statements)

References 40 publications

(48 reference statements)

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“…Genetic techniques for species identification based on multiple genes (rbcL & matK for plants; COBL Plant Working Group, 2009) or single-gene (CO1 for animal; Hebert et al, 2003) sequence similarity or phylogenies have been rapidly gaining wide use. BLAST, the nearest distance/similarity of sequences and phylogenetic tree based method have been used as bioinformatics tools along with molecular techniques for the identification of plants (Liu et al, 2012a;Liu et al, 2012b;Pang et al, 2012). In this study, BLAST search using both rbcL and matK primarily identified the query specimen as C. murale except BOLD search with matK gene sequence, which misidentified the specimen.…”

Section: Discussionmentioning

confidence: 99%

Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

Bafeel¹,

Arif²,

Al-Homaidan³

et al. 2012

IJB

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Chenopodium murale L. (Chenopodiaceae) is an erect annual herbaceous weed. This species is a threat for ecosystems worldwide as this annual-weed affects the growth and development of other plants by reducing the biological nitrogen-fixing ability. We evaluated the barcoding genes of the plastid region of C. murale [rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase) and matK (Maturase K)] for the success of PCR amplification, the differential inter-specific divergences and the ability of a single gene or combination of rbcL and matK genes to discriminate C. murale as individual species. Online nucleotide database-search using individually produced sequences of rbcL and matK gene of the plastid region primarily identified the specimen as C. murale with 100% sequence similarity. The single gene matK showed better resolution of the tree compared with the other phylogenetic-trees that were inferred from the single rbcL gene sequence or the combination of sequences of rbcL and matK. We found that single gene sequence of matK had high discrimination efficiency for the identification of the species C.

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Section: Discussionmentioning

confidence: 99%

Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

Bafeel¹,

Arif²,

Al-Homaidan³

et al. 2012

IJB

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“…The single pair of rbcL primers we used worked in gymnosperms, lycophytes, monilophytes, and angiosperms, as other studies have also found (e.g., [34]). Although other primers have been used to recover rbcL from ferns [87,96] and gymnosperms in DNA barcoding studies (e.g., [166]), a single set of primers that will amplify rbcL across land plants is of great practical use, facilitating recovery of the region from any unknown sample. In angiosperms, rbcL was recovered from an equal or greater number of samples per family than matK , except in Boraginaceae, in which rbcL was recovered from just one of 11 samples, which all worked for matK (Figure S2).…”

Section: Discussionmentioning

confidence: 99%

DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species

et al. 2013

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Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA–trnH, psbK–psbI, atpF–atpH) collected for a subset of Poa and Puccinellia species, only atpF–atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.

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“…Procurement of materials from other plant species was described previously [14], [71], [72]. Genomic DNA extraction was performed using the Plant Genomic DNA Extraction Kit according to the manufacturer′s protocol (Tiangen Biotech Co., China).…”

Section: Methodsmentioning

confidence: 99%

Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

et al. 2012

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BackgroundInternal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.Methodology/Principal FindingsIn this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.ConclusionsIdentification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.

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Assessing the potential of candidate DNA barcodes for identifying non‐flowering seed plants

Cited by 18 publications

References 40 publications

Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species

Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

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