Evaluation of six candidate DNA barcoding loci in <i>Ficus</i> (Moraceae) of China

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

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“…; CBOL Plant Working Group ; Li et al . ). Of the coding regions, matK provided higher species resolution (73.6%) than rbcL (60.5%) (Table ).…”

Section: Resultsmentioning

confidence: 97%

DNA barcoding of Orchidaceae in Korea

Kim

Bhandari

et al. 2013

Molecular Ecology Resources

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“…This distribution pattern was observed in other large genera such as Ficus L. (Moraceae) (Li et al . ) and Parnassia L. (Parnassiaceae) (Yang et al . ).…”

Section: Discussionmentioning

confidence: 99%

Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus

Alves

Chauveau

Eggers

et al. 2013

Molecular Ecology Resources

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DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.

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“…Liu, Zhang, et al (2012) showed a 100% identification using the psbA-trnH sequence in 38 species from the genus Rhododendron. Li, Chen, Wang, and Xiong (2012) discovered that the efficiency of the ITS sequence is 70% when examining 63 species in the genus Ficus. Yang, Wang, Möller, Gao, and Wu (2012) used ITS + psbA-trnH sequences to identify 30 species from the genus Parnassia with 90% efficiency.…”

Section: Introductionmentioning

confidence: 99%

The impact of genetic diversity on the accuracy of DNA barcoding to identify species: A study on the genus Phellodendron

Zhang

Wang

Zhao

et al. 2019

Ecology and Evolution

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DNA barcoding is widely used in species identification, but there is considerable controversy regarding the extent of sampling in research methods. Some scholars have proposed that this small sample size underestimates the intraspecific genetic diversity, which would impact on the accuracy of DNA barcoding to identify species. In study, we selected all Phellodendron species (including P. amurense Rupr., P. chinense Schneid., and P. chinense var. glabriusculum Schneid.) as the materials, collected 59 P. amurense samples from 35 populations greatly to represent the genetic diversity, and analyzed the haplotype, genetic distance, barcoding gap, and Neighbor‐Joining (NJ) trees based on psbA‐trnH and internal transcribed spacer gene sequences. Additionally, a sampling simulation was conducted to assess the correlation between genetic diversity and the number of populations. Finally, analysis of critical geographical populations was performed. Based on analysis of haplotype, genetic distance, barcoding gap, and NJ trees, we found that eight P. amurense samples impacted on the effectiveness of DNA barcoding, which genetic information were very important to identify Phellodendron species. Moreover, the result of the NJ tree analysis performed the small‐scale P. amurense sample size did not completely match the objective phylogenetic relationship in Phellodendron. In simulation sampling analysis, the data showed the genetic diversity indexes at the same population level gradually decreased and stabilized as the number of simulation sampling populations increased. We found that 1–2 samples from over 24 populations based on uniform geographical distribution could represent 80% of the genetic diversity of P. amurense and ensure authenticity and reliability of DNA barcoding. Thus, we proposed it is particularly important adequately samples to cover infraspecific genetic diversity in order to ensure identification accuracy of DNA barcoding.

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Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China

Cited by 56 publications

References 45 publications

DNA barcoding of Orchidaceae in Korea

DNA barcoding of Orchidaceae in Korea

Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus

The impact of genetic diversity on the accuracy of DNA barcoding to identify species: A study on the genus Phellodendron

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