Phylogenetic relationship of China Dendrobium species based on the sequence of the internal transcribed spacer of ribosomal DNA

Yuan, Zuli; Zhang, Jianyong; Liu, T.

doi:10.1007/s10535-009-0024-0

Cited by 19 publications

(14 citation statements)

References 13 publications

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“…D. fimbriatum and D. chrysotoxum have a close phylogenetic relationship [49], while in the present study, the two species were colonized by different xylariaceous fungi, indicating that different host plants in the same habitat might have preference and selectivity for their fungal partner.…”

Section: Discussioncontrasting

confidence: 44%

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

et al. 2013

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Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery.

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Section: Discussioncontrasting

confidence: 44%

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

et al. 2013

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“…In fact, ITS sequences were previously used to generate the first phylogeny of Rubus, which generally corresponded to their biogeography and polyploid, but not to their conventionally important morphological characters [19]. Our study has been congruent with the previous reports of Yuan et al [20] and Trung et al [14], who documented the relationship of Dendrobium species based on sequences characterization of the rDNA ITS region.…”

Section: The Phylogenetic Trees Based On Its-rdna Of 21 Ochna Samplessupporting

confidence: 89%

Identification of Vietnamese Ochna integerrima (Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence

Trang

Dong²,

Chung³

et al. 2018

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Ochna integerrima is a medicinal and ornamental plant, is widely distributed in Southeast Asia areas. In Vietnam, it has been ranked as the rare and endangered species due to its high demand trade of the beautiful species. In this study, total 21 Ochna samples, collected from the northern and southern areas, were used to characterize the morphological traits using morphological analyses and molecular tool. The results have revealed that the morphological characterization of flower and its quality of Yen Tu Ochna samples showed differences in comparison with the common Ochna and southern Ochna samples. To accurately distinguish genetic traits of the samples, we have sequenced the internal transcribed spacer (ITS) region (including ITS1, 5.8S) of 21 species. The results have disclosed the genetic correlations of the samples ranging from 96.25% to 100% among the studied Ochna samples, of which 5 samples include B1, B2, B3, B6 and N3.1 were divided into the separate groups. The current work is the first report in constructing a molecular database of Ochna for further assessment of inter-and intra-specific molecular diversity of Ochna species in Vietnam.

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“…However, differences between classical and molecular approaches were also reported in studies of Dendrobium spp. found in Taiwan (Tsai et al, 2004) and China (Yuan et al, 2009). The orchids of sections Breviflores and Pedilonum were placed in the same cluster as section Dendrobium (cluster I in Fig.…”

Section: Dendrobium) Was Closely Related To D Infundibulum (Section mentioning

confidence: 97%

“…In Dendrobium, the molecular phylogeny of several species has been studied using nucleotide sequences of both rDNA ITS (Burke et al, 2008;Tsai et al, 2004;Yuan et al, 2009) and the matK gene (Yukawa et al, 2000). However, the number of species included in each study was very limited owing to the range of species distributed in different regions (Australia, China and Taiwan).…”

Section: Introductionmentioning

confidence: 99%

“…However, the number of species included in each study was very limited owing to the range of species distributed in different regions (Australia, China and Taiwan). Moreover, the result of molecular phylogenetic analyses of Dendrobium in China (Wang et al, 2009;Yuan et al, 2009) and Taiwan (Tsai et al, 2004) were not well supported by the morphological classification, leading to the suggestion of separating some species into a new genus in Taiwan (Tsai et al, 2004). This suggests that molecular phylogeny is a valuable tool for supporting the classical taxonomy or for reclassification in some taxa.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic Relationship of Dendrobium Species in Thailand Inferred from Chloroplast matK Gene and Nuclear rDNA ITS Region

et al. 2015

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In Thailand, Dendrobium is the most popular crop grown for cut flowers and as a pot plant for local use and export. Some native species are used for hybrid production while some are specific to particular parts of the country and need to be conserved. The sequences of rDNA ITS (ITS1-5.8S-ITS2) and the matK gene were used to reconstruct the phylogenetic relationships of 27 native Dendrobium spp. in Thailand, which are composed of 9 sections: Breviflores, Callista, Dendrobium, Distichophyllum, Formosae, Pedilonum, Rhopalanthe, Stachyobium, and Strongyle. The average levels of nucleotide divergence (p-distances) of matK and rDNA ITS sequences were 1.3% and 11.2%, respectively. The topologies of the phylogenetic trees reconstructed based on matK and rDNA ITS sequences were slightly different. Use of the rDNA ITS sequence was shown to be a more authoritative systematic approach than use of the matK gene sequence in the genus Dendrobium. The result of the combined data (matK-rDNA ITS) was highly similar to the result from rDNA ITS. From rDNA ITS and combined data, the twenty-seven Dendrobium spp. were clearly grouped into two clades with some differences from the morphological classification. The present study provides the first molecular phylogeny of 27 native Dendrobium species in Thailand.

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Phylogenetic relationship of China Dendrobium species based on the sequence of the internal transcribed spacer of ribosomal DNA

Cited by 19 publications

References 13 publications

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

Identification of Vietnamese <i>Ochna integerrima</i> (Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence

Phylogenetic Relationship of <i>Dendrobium</i> Species in Thailand Inferred from Chloroplast <i>matK</i> Gene and Nuclear rDNA ITS Region

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Phylogenetic relationship of China Dendrobium species based on the sequence of the internal transcribed spacer of ribosomal DNA

Cited by 19 publications

References 13 publications

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

Identification of Vietnamese <i>Ochna integerrima</i>&nbsp;(Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence

Phylogenetic Relationship of <i>Dendrobium</i> Species in Thailand Inferred from Chloroplast <i>matK</i> Gene and Nuclear rDNA ITS Region

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Identification of Vietnamese <i>Ochna integerrima</i> (Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence