Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

Feng, Shi Ting; Jiang, Yan; Wang, Shang; Jiang, Mengying; Chen, Zhe; Ying, Qicai; Wang, Huizhong

doi:10.3390/ijms160921975

Cited by 67 publications

(74 citation statements)

References 54 publications

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“…Chrysotoxae formed two clades (1, 2), which indicated that sect. Chrysotoxae was probably polyphyletic, and this result was consistent with precious reports (Feng et al, 2015b). It was reported that sect.…”

Section: Figsupporting

confidence: 82%

“…Thus, it is necessary to exploit other barcode loci as supplementary molecular marker to distinguish these species. Due to their vegetative similarity, abundant species and lapped morphologic variation within some species (Xu et al, 2015), Dendrobium taxonomy is considered as the most complicated challenges in Orchidaceae (Feng et al, 2015b). As the findings of other molecular researches, this study also found that infrageneric taxa of Dendrobium were not monophyletic (Xiang et al, 2013;Feng et al, 2015a, b).…”

Section: Figsupporting

confidence: 55%

“…Dendrobium, which strongly endorsed the opinion that they should be contained in sect. Dendrobium (Feng et al, 2015b). Futhermore, D. catenatum was also grouped together with sect.…”

Section: Figmentioning

confidence: 98%

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Authentication of Chinese Herbal Medicines Dendrobium Species and Phylogenetic Study Based on nrDNA ITS Sequence

Wang¹

2018

IJAB

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Dendrobium plants are one of the most valuable traditional Chinese medicinal herbs. Because of excessive exploitation and habitat degradation, Dendrobium species are endangered. Moreover, during no flowering stages, it is very difficult and even impossible to distinguish Dendrobium species based on morphological characteristics. Therefore, exploiting other DNA barcodes as complementary molecular marker for distinguishing Dendrobium spp. are necessary. Hence, developing an uncomplicated and exact method for authenticating Dendrobium spp. is imperative. In this study, nuclear ribosomal DNA internal transcribed spacer (ITS) sequences of 320 samples from 73 Dendrobium spp. were analyzed. The average intra-and inter-specific genetic divergences were 0.007 and 0.220, respectively. The TaxonGap method indicated that between-species variation of about 80.9% of the species were higher than within-species variation. The neighbor-joining tree showed that 73 Dendrobium spp. were divided into four major clades. Phylogenetic relationships between Dendrobium spp. supported traditional morphological methods and previously published molecular data. This study indicated that ITS region was not only suitable for species identification, but also for phylogenetic analysis of Dendrobium. However, it was also found that ITS could not readily resolve all species determination problems in Dendrobium.

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Section: Figsupporting

confidence: 82%

Section: Figsupporting

confidence: 55%

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Authentication of Chinese Herbal Medicines Dendrobium Species and Phylogenetic Study Based on nrDNA ITS Sequence

Wang¹

2018

IJAB

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“…Numerous studies have focused on searching the most appropriate DNA loci for low taxonomic level studies of Dendrobium species 5, 6, 16 . However, due to limited loci or taxes sampled, some conclusions made in these studies are inconsistent.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Zhitao

Zhu

Pan

et al. 2017

Sci Rep

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Dendrobium is one of the largest genera in Orchidaceae, comprising about 800–1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots—trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ—should be used in the phylogenetic and identification studies of Dendrobium.

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“…An ideal DNA barcode could provide significant species discrimination and identification (Feng et al, 2014; Gong et al, 2016; Nigro et al, 2016). We used two different analyses to evaluate the discrimination rates between species and sections within Aceraceae.…”

Section: Discussionmentioning

confidence: 99%

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Han

Duan

et al. 2016

Front. Plant Sci.

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Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).

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Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

Cited by 67 publications

References 54 publications

Authentication of Chinese Herbal Medicines Dendrobium Species and Phylogenetic Study Based on nrDNA ITS Sequence

Authentication of Chinese Herbal Medicines Dendrobium Species and Phylogenetic Study Based on nrDNA ITS Sequence

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

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