Genetic polymorphism of Japanese cultivated Rheum species in the internal transcribed spacer region of nuclear ribosomal DNA

Asanuma, Mai; Zhu, Shu; Okura, Naoki; Cai, Shao‐Qing; Yoshimatsu, Kayo; Komatsu, Kenshi

doi:10.1007/s11418-019-01298-4

Cited by 10 publications

(9 citation statements)

References 20 publications

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“…Anthraquinones have anti-inflammatory, antitumor, antiviral, anti-obesity, and anticoagulant properties [ 11 ]. In recent years, the wild stock of this species has decreased more rapidly than ever, and most natural populations have been destroyed in order to meet the commercial demand for the rhubarb species [ 12 ]. Efforts are being made to understand the biology of the crop and to replace the traditional approaches of R. palmatum cultivation with scientific practices.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Endophyte Diversity of Rheum palmatum from Different Production Areas in Gansu Province of China and the Association with Secondary Metabolite

et al. 2021

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Investigations of the differences in the metabolites of medicinal plants have typically focused on the effects of external environmental factors. However, little is known about the relationship between endophytes diversity and host metabolites. We used high-throughput sequencing methods to compare the endophyte diversity of Rheum palmatum from eight different production areas in Gansu Province of China and to analyze the association between those areas and five secondary metabolites (aloe-emodin, rhein, emodin, chrysophanol, and physcion). The results show that the diversity and OTUs (Operational taxonomic units) abundance of endophytic fungi and bacteria of R. palmatum differed according to production area. Spearman analysis showed that the five secondary metabolites of R. palmatum were positively correlated with the diversity and abundance of endophytic fungi. Comparing both space and environmental differences to determine influences on community structure, VPA analysis revealed that geographic factors explained more difference in community composition of fungal and bacterial endophytes than climate factors. PICRUSt and FUNGuild predictive analysis indicated that metabolites were the primary components of endophytic bacteria in all samples, while the function of endophytic fungi was composed of dominant trophic modes (saprotroph and pathotroph), and relative abundances were different. Our results help elucidate the correlation of plant–microbe interactions and offer pivotal information to reveal the role of endophytes in the production of R. palmatum and its important secondary metabolite.

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Section: Introductionmentioning

confidence: 99%

Analysis of Endophyte Diversity of Rheum palmatum from Different Production Areas in Gansu Province of China and the Association with Secondary Metabolite

et al. 2021

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“…The highly repetitive nrDNA ITS exists in thousands of copies, and its loci are prone to loss-of-function mutations, such as insertions, deletions, or code shifts, during the evolutionary process, resulting in pseudogenes. Although there are some reports about ITS pseudogenes in some plants (Buckler and Holtsford, 1996 ; Muir et al, 2001 ; Razafimandimbison et al, 2004 ; Wei and Wang, 2004 ; Harpke and Peterson, 2006 , 2008a ; Zheng et al, 2008 ; Xiao et al, 2010 ; Camila De Sousa et al, 2011 ; Zhou et al, 2013 ; Xu et al, 2015 , 2017 ; Huang et al, 2016 ; Asanuma et al, 2019 ), the severe heterozygosity of ITS sequences can lead to a search for alternative molecular markers. This is also one of the reasons why there have been fewer studies on pseudogenes.…”

Section: Discussionmentioning

confidence: 99%

“…Hence, intra-individual polymorphism has generally been considered an exception. However, with the development of sequencing technology, some studies have revealed intra-individual ITS polymorphisms in a range of taxa (Muir et al, 2001 ; Razafimandimbison et al, 2004 ; Wei and Wang, 2004 ; Harpke and Peterson, 2006 , 2008a ; Zheng et al, 2008 ; Xiao et al, 2010 ; Camila De Sousa et al, 2011 ; Zhou et al, 2013 ; Xu et al, 2015 , 2017 ; Huang et al, 2016 ; Asanuma et al, 2019 ; Li et al, 2019 ), including non-hybrid diploids. Some ITS copies may even become pseudogenes due to functional degradation.…”

Section: Introductionmentioning

confidence: 99%

Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes

et al. 2022

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The internal transcribed spacer (ITS) is one of the most extensively sequenced molecular markers in plant systematics due to its generally concerted evolution. While non-concerted evolution has been found in some plant taxa, such information is missing in Lycium. Molecular studies of six species and two variants of the genus Lycium revealed high levels of intra- and inter-individual polymorphism in the ITS, indicating non-concerted evolution. All genomic DNA ITS paralogues were identified as putative pseudogenes or functional paralogues through a series of comparisons of sequence features, including length and substitution variation, GC content, secondary structure stability, and the presence of conserved motifs in the 5.8S gene, and the rate of evolution. Approximately, 60% of ITS pseudogenes could be easily detected. Based on phylogenetic analysis, all pseudogenes were highly distinct from their corresponding functional copies, tended to evolve neutrally, and clustered randomly together in the evolutionary tree. The results probably suggest that this ITS non-concerted evolution is related to the recent divergence between tandem repeats within the Lycium genome and hybridization between species. Our study complements those of pseudogenes in plant taxa and provides a theoretical basis for the phylogeny and genetic origin of the genus Lycium while having important implications for the use of ITS molecular markers for phylogenetic reconstruction.

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“…The medicinal properties of plants determine their functions in curing diseases. For instance, G. uralensis is mainly used for cough relief, heat clearing, and detoxification [19]; R. altaicum can be used for diarrhea, blood stasis, and constipation [20]; and F. sinkiangensis acts against indigestion, gastropathy, and insects [21]. Examining these properties allows us to better understand how plants respond to their living habitats and which parts of the plants can provide value.…”

Section: Medicinal Value Of Medicinal Plants and Their Community Charmentioning

confidence: 99%

Vegetation Characteristics and Response to the Soil Properties of Three Medicinal Plant Communities in Altay Prefecture, China

et al. 2020

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Plant communities and their environments are a vital part of synecology research. In this study, we investigated the characteristics of three typical medicinal perennial herbs, Glycyrrhiza uralensis, Rheum altaicum, and Ferula sinkiangensis, and examined their response to local soil properties in Altay Prefecture, China. A total of 29 species belonging to 15 families and 25 genera were recorded. In terms of the target medicinal plants, the importance value was low and community structures were exceedingly simple. Quantitative classification based on WARD cluster analysis suggested that each medicinal plant can be classified into one of three types: annual herbaceous, perennial herbaceous, and subshrub or shrub. Interestingly, the plants gradually transformed from exhibiting nonresistance to xerophytes or halophytes. An investigation of the soil properties beneath the medicinal plants showed that nutrients in black soil were much more abundant than those in sandy and saline soil. Except for leaching phenomenon, the nutrient contents in the soil surface layer (0–10 cm) were higher than those in deep layers (10–20 cm and 20–40 cm), and to some extent, the nutrient contents were inversely proportional to the depth of the soil. The redundancy analysis (RDA) results of the medicinal plants and their relationship with soil properties indicated that the main soil variables impacting the distribution of G. uralensis were available potassium (AK), aspect (ASP), soil moisture (SM), total nitrogen (TN), and total phosphorus (TP); SM, electric conductivity (EC), elevation (ELE), ASP, pH value (pH), available nitrogen (AN), soil organic content (SOC), and the carbon/nitrogen (C/N) ratio had positive effects on the distribution of R. altaicum. F. sinkiangensis grew better in habitats with high contents of SM, EC, TN, AN, available phosphorus (AP), total potassium (TK), and AK. This study aimed at providing effective suggestions for artificial cultivation, conservation, and resilience of Chinese medicinal plants.

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Genetic polymorphism of Japanese cultivated Rheum species in the internal transcribed spacer region of nuclear ribosomal DNA

Cited by 10 publications

References 20 publications

Analysis of Endophyte Diversity of Rheum palmatum from Different Production Areas in Gansu Province of China and the Association with Secondary Metabolite

Analysis of Endophyte Diversity of Rheum palmatum from Different Production Areas in Gansu Province of China and the Association with Secondary Metabolite

Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes

Vegetation Characteristics and Response to the Soil Properties of Three Medicinal Plant Communities in Altay Prefecture, China

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