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Wang D, Huang Y, Rui L, Du H, Qi J, Ma M, Zhou N. Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments. Genes (Basel) 2023; 14:1754. [PMID: 37761894 PMCID: PMC10530812 DOI: 10.3390/genes14091754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Genetic structure and genetic differentiation were explored using haplotype distribution maps and genetic distance matrices. A total of 15 haplotypes were identified in the 32 populations of P. polyphylla var. yunnanensis. Five unique haplotypes were identified from the fourteen haplotypes of the cultivated populations, while only one unique haplotype was identified from the ten haplotypes of the wild populations. The haplotype richness and genetic diversity of the cultivated populations were higher than those of the wild populations (HT = 0.900 vs. 0.861). In addition, there were no statistically significant correlations between geographic distance and genetic distance in the cultivated populations (r = 0.16, p > 0.05), whereas there was a significant correlation between geographical distance and genetic structure in the wild populations (r = 0.32, p > 0.05), indicating that there was a geographical and genetic connection between the wild populations. There was only 2.5% genetic variation between the wild populations and cultivated populations, indicating no obvious genetic differentiation between the wild and cultivated populations. Overall, the genetic background of the cultivated populations was complex, and it was hypothesized that the unique haplotypes and higher diversity of the cultivated populations were caused by the mixed provenance of the cultivated populations.
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Affiliation(s)
- Dan Wang
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Yu Huang
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
- College of Pharmacy, Dali University, Dali 671000, China
| | - Lu Rui
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Huihui Du
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Junsheng Qi
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Mingguo Ma
- Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nong Zhou
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
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Zhou N, Xu L, Park SM, Ma MG, Choi SE, Si C. Genetic Diversity, Chemical Components, and Property of Biomass Paris polyphylla var. yunnanensis. Front Bioeng Biotechnol 2021; 9:713860. [PMID: 34368107 PMCID: PMC8339996 DOI: 10.3389/fbioe.2021.713860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Paris polyphylla var. yunnanensis is a kind of biomass resource, which has important medicinal and economical values with a huge market. This review article aims to summarize the recent development of biomass P. polyphylla var. yunnanensis. The genetic diversity and chemical components of biomass P. polyphylla var. yunnanensis were reviewed based on the literature. Both the genetic diversity and genetic structure of biomass P. polyphylla var. yunnanensis were compared by using molecular marker technologies. All the extraction processes, harvest time, and drying methods on the chemical components were summarized in detail. The differences of arbuscular mycorrhizal fungi on the infection rate, diosgenin content, microorganisms, enzyme activities, rhizospheric environment, and endogenous hormones were discussed. This review article is beneficial for the applications of biomass P. polyphylla var. yunnanensis as a biomass resource in the biomedical field.
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Affiliation(s)
- Nong Zhou
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-Region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Lingfeng Xu
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-Region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Sun-Min Park
- Department of Forest Biomaterials Engineering, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ming-Guo Ma
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-Region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
- Beijing Key Laboratory of Lignocellulosic Chemistry, Research Center of Biomass Clean Utilization, Engineering Research Center of Forestry Biomass Materials and Bioenergy, College of Materials Science and Technology, Beijing Forestry University, Beijing, China
| | - Sun-Eun Choi
- Department of Forest Biomaterials Engineering, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, South Korea
| | - Chuanling Si
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science and Technology, Tianjin, China
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Chen Z, Anane RF, Wang Z, Gao L, Chen L, Li S, Wen G, Zhao M. Complete genome sequence analysis of a novel coguvirus isolated from Paris polyphylla var. yunnanensis. Arch Virol 2021; 166:2045-2050. [PMID: 33944994 DOI: 10.1007/s00705-021-05087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
A novel negative-stranded (ns) RNA virus tentatively named "Yunnan paris negative-stranded virus" (YPNSV), was isolated from Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. YPNSV has a bipartite genome that consists of a negative-stranded (ns) RNA1 encoding the viral RNA-dependent RNA polymerase (RdRp, p251), an ambisense RNA2 coding for the putative movement protein (MP, p46) and nucleocapsid protein (NP, p39), with the two open reading frames separated by a long intergenic region that is rich in A and U. Sequence comparisons showed that the RdRp, MP, and NP of YPNSV are most similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4%, and 60.9% amino acid sequence identity, respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP showed that YPNSV clustered in a clade with coguviruses and that its closest known relative is WCLaV-2. Based on the above results, YPNSV should be regarded as a new member of genus Coguvirus, family Phenuiviridae.
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Affiliation(s)
- Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Rex Frimpong Anane
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.,State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Zhe Wang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Lu Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China. .,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.
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