A comparative plastomics approach reveals available molecular markers for the phylogeographic study of <i>Dendrobium huoshanense</i>, an endangered orchid with extremely small populations

Niu, Zhitao; Hou, Zhenyu; Wang, Mengting; Ye, Meirong; Zhang, Benhou; Xue, Quan; Liu, Wei; Ding, Xiaoyu

doi:10.1002/ece3.6277

Cited by 8 publications

(6 citation statements)

References 56 publications

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“…Hybridization, a driver of plant evolution, is common among terrestrial orchids [ 35 ]. Although dust-like seeds have the capacity to travel long distance [ 36 – 38 ], the results of this study showed that Bulbophyllum AN clade has diverged completely from SA clade in the late Oligocene (21.50–30.12 mya) [ 18 ]. Because the results of the JML software have ruled out the possibility of hybridization between the two clades [ 39 ], Bulbophyllum AN and SA clades have evolved independently for at least 25.81 million years.…”

Section: Discussionmentioning

confidence: 99%

Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Yang

Zhang

et al. 2022

BMC Plant Biol

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Background Because chloroplast (cp) genome has more conserved structures than nuclear genome and mitochondrial genome, it is a useful tool in estimating the phylogenetic relationships of plants. With a series of researches for cp genomes, there have been comprehensive understandings about the cp genome features. The genus Bulbophyllum widely distributed in Asia, South America, Australia and other places. Therefore, it is an excellent type genus for studying the effects of geographic isolation. Results In this study, the cp genomes of nine Bulbophyllum orchids were newly sequenced and assembled using the next-generation sequencing technology. Based on 19 Asian (AN) and eight South American (SA) Bulbophyllum orchids, the cp genome features of AN clade and SA clade were compared. Comparative analysis showed that there were considerable differences in overall cp genome features between two clades in three aspects, including basic cp genome features, SSC/IRB junctions (JSBs) and mutational hotspots. The phylogenetic analysis and divergence time estimation results showed that the AN clade has diverged from the SA clade in the late Oligocene (21.50–30.12 mya). After estimating the occurrence rates of the insertions and deletions (InDels), we found that the change trends of cp genome structures between two clades were different under geographic isolation. Finally, we compared selective pressures on cp genes and found that long-term geographic isolation made AN and SA Bulbophyllum cp genes evolved variably. Conclusion The results revealed that the overall structural characteristics of Bulbophyllum cp genomes diverged during the long-term geographic isolation, and the crassulacean acid metabolism (CAM) pathway may play an important role in the Bulbophyllum species evolution.

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Section: Discussionmentioning

confidence: 99%

Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Yang

Zhang

et al. 2022

BMC Plant Biol

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“…Among them, there are 39 species of Dendrobium with medicinal purposes, including D. huoshanense ( Chiang et al, 2012 ; Ye et al, 2021 ). However, the natural distribution of D. huoshanense is relatively narrow, because of its preference for a cool and moist environment, and high environmental requirements ( Liu et al, 2007 ; Qin et al, 2008 ; Niu et al, 2020 ). Wild D. huoshanense mainly grows as an epiphytic on the cliffs beside rivers and valleys at a slight altitude ranging between 200 and 1,200 m. In view of its strict requirements on the environment, D. huoshanense is currently endemic to the Da-bie Mountains, with Huoshan in the Anhui Province as the center of distribution ( Zha et al, 2007d ; Zheng et al, 2011 ; Wang et al, 2012 ; Wu et al, 2016 ).…”

Section: Resourcementioning

confidence: 99%

Dendrobium huoshanense C.Z.Tang et S.J.Cheng: A Review of Its Traditional Uses, Phytochemistry, and Pharmacology

et al. 2022

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Dendrobium huoshanense, a traditional medicinal and food homologous plant, belongs to the family Orchidaceae and has a long history of medicinal use. It is reported that the stem of D. huoshanense has a variety of bioactive ingredients such as polysaccharides, flavonoids, sesquiterpenes, phenols, etc. These bioactive ingredients make D. huoshanense remarkable for its pharmacological effects on anti-tumor, immunomodulation, hepatoprotective, antioxidant, and anticataract activities. In recent years, its rich pharmacological activities have attracted extensive attention. However, there is no systematic review focusing on the chemical compositions and pharmacological effects of D. huoshanense. Therefore, the present review aims to summarize current research on the chemical compositions and pharmacological activities of D. huoshanense. This study provides valuable references and promising ideas for further investigations of D. huoshanense.

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“…However, people over-excavate and conduct commercial trade for profit, thus causing serious damage to the wild resources [ 65 ]. This leads to a decline in the genetic differentiation among the Dendrobium species [ 66 ].…”

Section: Discussionmentioning

confidence: 99%

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum

Zheng

et al. 2022

Genes

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Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (HE) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins.

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A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense, an endangered orchid with extremely small populations

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 8 publications

References 56 publications

Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Dendrobium huoshanense C.Z.Tang et S.J.Cheng: A Review of Its Traditional Uses, Phytochemistry, and Pharmacology

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum

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