DNA barcoding: a new tool for palm taxonomists?

Jeanson, Matthieu; Labat, Jean-Noël; Little, Damon P.

doi:10.1093/aob/mcr158

Cited by 53 publications

(58 citation statements)

References 47 publications

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Section: Resultsmentioning

confidence: 64%

“…Although not comparable in all cases, the median Podocarpaceae sequence is of higher quality than the average sequence reported for angiosperms across all three markers [61], [89], [90]. The largest comparable difference between literature reports and newly generated Podocarpaceae sequences was observed in nrITS2 (0.829 versus 0.924; [89]). The high quality of Podocarpaceae matK sequences is notable, but the gymnosperm specific primers [52] used to generate the matK sequences make direct comparisons to published values for angiosperms tenuous.…”

Section: Resultsmentioning

confidence: 64%

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DNA Barcode Identification of Podocarpaceae—The Second Largest Conifer Family

2013

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We have generated matK, rbcL, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (B 30 = 0.596–0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (p = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p–distance > minimum interspecific p–distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (p = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (p = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (p = 0.27).

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Section: Resultsmentioning

confidence: 64%

Section: Resultsmentioning

confidence: 64%

DNA Barcode Identification of Podocarpaceae—The Second Largest Conifer Family

2013

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“…Amplification and sequencing of the matK barcoding region is difficult due to high sequence variability in the primer binding sites (Hollingsworth et al, 2011). Currently, there are three popular matK primer pairs available to amplify approximately the same region of the gene: 390F and 1326R (Sun et al, 2001; Cuénoud et al, 2002), XF and 5R (Ford et al, 2009), and 1R_KIM and 3F_KIM (Hollingsworth et al, 2009; Jeanson et al, 2011). Kress et al (2009) used these three primer pairs to amplify DNA barcodes from 296 shrub and tree species.…”

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confidence: 99%

Universal multiplexable matK primers for DNA barcoding of angiosperms

2016

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Premise of the study:PCR amplification of the matK barcoding region is often difficult when dealing with multiple angiosperm families. We developed a primer cocktail to amplify this region efficiently across angiosperm diversity.Methods and Results:We developed 14 matK primers (seven forward, seven reverse) for multiplex PCR, using sequences available in GenBank for 178 taxa belonging to 123 genera in 41 families and 18 orders. Universality of these new multiplexed primers was tested with 53 specimens from 44 representative angiosperm families in 23 different orders. Our primers showed high PCR amplification and sequencing success.Conclusions:These results show that our newly developed primers are highly effective for multiplex PCR and can be employed in future barcode projects involving taxonomically diverse samples across angiosperms. Using multiplex primers for barcoding will reduce the cost and time needed for PCR amplification.

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“…Although mini‐barcode F produced the highest quality sequences, these quality values are lower than those typically reported for rbcL a (Little ; Jeanson et al . ; Aubriot et al . ).…”

Section: Discussionmentioning

confidence: 99%

A DNA mini‐barcode for land plants

Little

2013

Molecular Ecology Resources

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Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).

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DNA barcoding: a new tool for palm taxonomists?

Cited by 53 publications

References 47 publications

DNA Barcode Identification of Podocarpaceae—The Second Largest Conifer Family

DNA Barcode Identification of Podocarpaceae—The Second Largest Conifer Family

Universal multiplexable matK primers for DNA barcoding of angiosperms

A DNA mini‐barcode for land plants

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