Phylogeography of endangered Dendrobium moniliforme in East Asia based on mitochondrial DNA sequence variations

Ye, Meirong; Liu, Wei; Xue, Quan; Yan, Wenjin; Hou, Beiwei; Luo, Jing; Ding, Xiaoyu

doi:10.1007/s10531-017-1324-x

Cited by 9 publications

(8 citation statements)

References 43 publications

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“…The other studies had reported the similar results of D. nobile (Zhang et al 2013;. Similar reports in D.moniliforme, another species of the Dendrobium genus (Ye et al 2017). The reasons were considered that there had been high genetic differentiation in the long-term evolution process owing to geographic isolation, fragmented distribution and lack of exchange between natural populations.…”

Section: Discussionsupporting

confidence: 76%

“…Molecular markers have been developed and a variety of molecular markers have been used to detect genetic diversity and genetic relationships among species in the genus Dendrobium to date, including random-ampli ed polymorphic DNA (RAPD) (Zhu et al 2011), inter simple sequence repeat (ISSR) ), simple sequence repeat (SSR) (Lu et al 2013; Kang et al 2015), sequence related ampli ed polymorphism (SRAP) (Feng et al 2014), inter primer binding repeats site (iPBs) (Cui et al 2020), target region ampli cation polymorphism (trap) (Feng et al 2015), sequence-characterized ampli ed regions (scar) (Zheng et al 2021), these markers are based on electrophoretic map. Other markers are based on sequence differences, including nuclear genome such as ITS, chloroplast genome, including matK, rbcL, psbA-trnH and mitochondrial genome (Ye et al 2017;Wang et al 2018;Nguyen et al 2020). These studies showed that highly genetic differentiation and rich genetic diversity existed among different Dendrobium species.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Ye²,

Zeng³

et al. 2021

Preprint

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Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access genetic diversity because of its high-throughput and cost-effective in molecular markers. The goal of this study was to employ the GBS technique for diversity evaluation of D. nobile and determine genetic differences between populations. A total of 129 accessions of D. nobile collected originally between 2019 and 2020 from 10 imitation-wild cultivated populations growing in Sichuan, Guizhou and Yunnan of southwestern China were sequenced, a total of 135G clean reads and a total of 836,786 SNPs of high quality data was yielded and were used for final analysis of genetic diversity and population structure. The quality value 20(Q20) ≥ 92.61%, the quality value 30(Q30) ≥ 82.38%. The GC contents distributed between 37.58% and 38.82%. It was also found that more transitions than transversions, and the ratio of transition/transversion varied from 1.804 to 1.911. By the methods of STRUCTURE, the most appropriate number was found to be k=3, all accessions of D. nobile were classified into three groups, excepts for 14 accessions belonging to admixed group. Phylogenetic tree and principal component analysis (PCA) were consistent with the result. The first two principal components explained a total of 23.25% of the variation by PCA. The genetic diversity of ML population showed the lower genetic diversity as indicated by the effective number of alleles (Ne) = 1.287, polymorphism information content (PIC) = 0.141, and Shannon's information index (I) = 0.205, while WT population showed slightly higher genetic diversity by the Ne =1.512, PIC =0.256, and I =0.360. ML population and other nine populations (FB, FM, FX, LJ, SJ, SP, WL, WT and XM) were the most divergent between them respectively owing to all pairwise Fst values above 0.25, while FM population and FX population were considered identical because the pairwise Fst value was 0.0 between the two populations. Correlation analysis showed that highly significant correlation was observed between genetic distance and actual geographical distance (r = 0.854, P < 0.0001), indicating that the genetic differentiation of the 10 D.nobile populations conformed to the geographical isolation model. Analysis of molecular variance (AMOVA) revealed that the genetic variation was greater within populations (87.8%) than among populations (12.2%). This confirmed that intra-population variation was the main source of genetic variation in 10 D. nobile populations. The results also showed that Nm = 1.799 > 1, indicating that there was gene exchange between different populations. Analysis of unweighted pair-group method with arithmetic mean (UPGMA) suggested that the 10 populations were classified into three groups (Group I, Group II and Group III), Group III could be further divided into two subgroups (Group IIIa and Group IIIb). The results will not only provide valuable information for the level of genetic diversity of D.nobile growing in southwestern of China but also help for formulation of strategies for resource protection and utilization. Moreover, GBS appears as an efficient tool to detect intra-population variation.

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Section: Discussionsupporting

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Ye²,

Zeng³

et al. 2021

Preprint

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“…The three highest diversity regions were ycf1, ndhF-rpl32 and trnE(UUC)-trnT(GGU), and the Pi values were 0.10867, 0.10576 and 0.10574, respectively, which were the only three regions whose Pi values were over 0.10000. These regions are more suitable for the study of genus levels, and have been widely used as molecular markers in previous phylogenetic studies [65][66][67], and easier to align than nrITS. In addition, we chose the ten regions with the highest Pi values for the phylogenetic analysis.…”

Section: Nucleotide Diversity Analysismentioning

confidence: 99%

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

Xie

Guo

et al. 2020

Plants

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Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.

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“…These mountain chains differ topographically and ecologically, exhibiting variations in temperature, precipitation and humidity (Figure 5; Li et al., 2013). Combined with the similar phylogeographical structure detected in several other plants, including Eurycorymbus cavaleriei , Juglans cathayensis and Dendrobium moniliforme , the data collectively suggested that the obvious genetic differentiation and highly structured distribution of plant species in Central and East China were more affected by the orographical isolation effects associated with scattered mountain chains than the limited tectonic events that have occurred in this region (Bai et al., 2014; Wang et al., 2009; Ye et al., 2017). Overall, the different evolutionary histories of these lineages on the Chinese mainland may reflect variations in the development of their related floristic regions, which shaped the current distribution pattern of plant diversity (Kreft & Jetz, 2010).…”

Section: Discussionmentioning

confidence: 65%

Biogeographical divides delineated by the three‐step landforms of China and the East China Sea: Insights from the phylogeography of Kerria japonica

Luo

et al. 2020

Journal of Biogeography

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Aim East Asia exhibits complex geomorphological and climatic characteristics. The aim of this study was to test whether the so‐called three‐step landforms of China, together with the East China Sea (ECS), have acted to shape specific phylogeographical patterns and affected the biogeographical history of the species belonging to the East Asian Flora. Location China and Japan. Taxon Kerria japonica (L.) DC. Methods Three chloroplast DNA regions and 15 nuclear microsatellite (nSSR) loci were sequenced and genotyped in 576/450 individuals of K. japonica. Phylogeographical analyses were performed to assess the genetic structure, historical gene flow and demographical history of these individuals, and climatic factors were examined to determine their effects on phylogeographical breaks. Furthermore, time‐calibrated phylogenetic trees and ancestral range reconstruction were used to infer the biogeographical history of K. japonica. Potential habitats at present and during the last glacial maximum (LGM) were identified using ecological niche modelling. Results Distinct phylogeographical breaks were found across the ECS and along the boundary of the three‐step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. The results of molecular dating and ancestral range reconstruction indicated that K. japonica originated in North America during the mid‐Miocene (14.76 Ma), and intra‐specific diversification began in the late Miocene (7.78 Ma). Compared to the relatively stable distribution range of Chinese populations, Japanese populations experienced range expansion after the LGM in response to Quaternary climate change. Main conclusions Kerria japonica has a complex biogeographical history, with a mid‐Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra‐specific diversification was probably associated with Asian monsoon intensifications, while exposure to the ECS floor facilitated the formation of the Japanese lineage in the late Miocene. The spatiotemporal population differentiation on the Chinese mainland demonstrates the significant role of biogeographical divides delineated by the three‐step landforms of China and provides clues to understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China and East China.

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Phylogeography of endangered Dendrobium moniliforme in East Asia based on mitochondrial DNA sequence variations

Cited by 9 publications

References 43 publications

Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

Biogeographical divides delineated by the three‐step landforms of China and the East China Sea: Insights from the phylogeography of Kerria japonica

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