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Chen M, Li L, Wang S, Wang P, Li Y. Transcriptome sequencing and screening of genes related to the MADS-box gene family in Clematis courtoisii. PLoS One 2024; 19:e0294426. [PMID: 38315679 PMCID: PMC10843124 DOI: 10.1371/journal.pone.0294426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/31/2023] [Indexed: 02/07/2024] Open
Abstract
The MADS-box gene family controls plant flowering and floral organ development; therefore, it is particularly important in ornamental plants. To investigate the genes associated with the MADS-box family in Clematis courtoisii, we performed full-length transcriptome sequencing on C. courtoisii using the PacBio Sequel third-generation sequencing platform, as no reference genome data was available. A total of 12.38 Gb of data, containing 9,476,585 subreads and 50,439 Unigenes were obtained. According to functional annotation, a total of 37,923 Unigenes (75.18% of the total) were assigned with functional annotations, and 50 Unigenes were identified as MADS-box related genes. Subsequently, we employed hmmerscan to perform protein sequence similarity search for the translated Unigene sequences and successfully identified 19 Unigenes associated with the MADS-box gene family, including MIKC*(1) and MIKCC (18) genes. Furthermore, within the MIKCC group, six subclasses can be further distinguished.
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Affiliation(s)
- Mingjian Chen
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Linfang Li
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shu’an Wang
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Peng Wang
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ya Li
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Zhao Z, Zhang H, Wang P, Yang Y, Sun H, Li J, Chen X, Li J, Ji N, Feng H, Zhao S. Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains. PLoS One 2023; 18:e0285754. [PMID: 37205665 DOI: 10.1371/journal.pone.0285754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
Investigating the genetic diversity and population structure is important in conserving narrowly distributed plants. In this study, 90 Clematis acerifolia (C. acerifolia) plants belonging to nine populations were collected from the Taihang Mountains in Beijing, Hebei, and Henan. Twenty-nine simple sequence repeats (SSR) markers developed based on RAD-seq data were used to analyze the genetic diversity and population structure of C. acerifolia. The mean PIC value for all markers was 0.2910, indicating all SSR markers showed a moderate degree of polymorphism. The expected heterozygosity of the whole populations was 0.3483, indicating the genetic diversity of both C. acerifolia var. elobata and C. acerifolia were low. The expected heterozygosity of C. acerifolia var. elobata (He = 0.2800) was higher than that of C. acerifolia (He = 0.2614). Genetic structure analysis and principal coordinate analysis demonstrated that C. acerifolia and C. acerifolia var. elobata showed great genetic differences. Molecular variance analysis (AMOVA) demonstrated that within-population genetic variation (68.31%) was the main contributor to the variation of the C. acerifolia populations. Conclusively, C. acerifolia var. elobata had higher genetic diversity than C. acerifolia, and there are significant genetic differences between C. acerifolia and C. acerifolia var. elobata, and small genetic variations within the C. acerifolia populations. Our results provide a scientific and rational basis for the conservation of C. acerifolia and provide a reference for the conservation of other cliff plants.
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Affiliation(s)
- Zhengnan Zhao
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Henan Institute of Science and Technology, College of Life Science and Technology, Xinxiang, Henan, China
| | - Yuan Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hongyan Sun
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Jinyu Li
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Xiao Chen
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Jun Li
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Naizhe Ji
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Hui Feng
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Shiwei Zhao
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
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Qian R, Hu Q, Ma X, Zhang X, Ye Y, Liu H, Gao H, Zheng J. Comparative transcriptome analysis of heat stress responses of Clematis lanuginosa and Clematis crassifolia. BMC PLANT BIOLOGY 2022; 22:138. [PMID: 35321648 PMCID: PMC8941805 DOI: 10.1186/s12870-022-03497-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Clematis species are attractive ornamental plants with a variety of flower colors and patterns. Heat stress is one of the main factors restricting the growth, development, and ornamental value of Clematis. Clematis lanuginosa and Clematis crassifolia are large-flowered and evergreen Clematis species, respectively, that show different tolerance to heat stress. We compared and analyzed the transcriptome of C. lanuginose and C. crassifolia under heat stress to determine the regulatory mechanism(s) of resistance. RESULTS A total of 1720 and 6178 differentially expressed genes were identified from C. lanuginose and C. crassifolia, respectively. The photosynthesis and oxidation-reduction processes of C. crassifolia were more sensitive than C. lanuginose under heat stress. Glycine/serine/threonine metabolism, glyoxylic metabolism, and thiamine metabolism were important pathways in response to heat stress in C. lanuginose, and flavonoid biosynthesis, phenylalanine metabolism, and arginine/proline metabolism were the key pathways in C. crassifolia. Six sHSPs (c176964_g1, c200771_g1, c204924_g1, c199407_g2, c201522_g2, c192936_g1), POD1 (c200317_g1), POD3 (c210145_g2), DREB2 (c182557_g1), and HSFA2 (c206233_g2) may be key genes in the response to heat stress in C. lanuginose and C. crassifolia. CONCLUSIONS We compared important metabolic pathways and differentially expressed genes in response to heat stress between C. lanuginose and C. crassifolia. The results increase our understanding of the response mechanism and candidate genes of Clematis under heat stress. These data may contribute to the development of new Clematis varieties with greater heat tolerance.
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Affiliation(s)
- Renjuan Qian
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Qingdi Hu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
| | - Xiaohua Ma
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
| | - Xule Zhang
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
| | - Youju Ye
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
| | - Hongjian Liu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
| | - Handong Gao
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jian Zheng
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005 Zhejiang China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021 Wenzhou, China
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Hu Q, Qian R, Zhang Y, Zhang X, Ma X, Zheng J. Physiological and Gene Expression Changes of Clematis crassifolia and Clematis cadmia in Response to Heat Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:624875. [PMID: 33841457 PMCID: PMC8034387 DOI: 10.3389/fpls.2021.624875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Clematis is a superior perennial ornamental vine known for varied colors and shapes of its flowers. Clematis crassifolia is sensitive to high temperature, whereas Clematis cadmia has a certain temperature adaptability. Here we analyzed the potential regulatory mechanisms of C. crassifolia and C. cadmia in response to heat stress by studying the photosynthesis, antioxidant parameters, amino acids, and gene expression patterns under three temperature treatments. Heat stress caused the fading of leaves; decreased net photosynthetic rate, stomatal conductance, superoxide dismutase, and catalase activity; increased 13 kinds of amino acids content; and up-regulated the expression of seven genes, including C194329_G3, C194434_G1, and C188817_g1, etc., in C. crassifolia plants. Under the treatments of heat stress, the leaf tips of C. cadmia were wilted, and the net photosynthetic rate and soluble protein content decreased, with the increase of 12 amino acids content and the expression of c194329_g3, c194434_g1, and c195983_g1. Our results showed that C. crassifolia and C. cadmia had different physiological and molecular response mechanisms to heat stress during the ecological adaptation.
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Affiliation(s)
- Qingdi Hu
- Zhejiang Institute of Subtropical Crops, Wenzhou, China
| | - Renjuan Qian
- Zhejiang Institute of Subtropical Crops, Wenzhou, China
| | - Yanjun Zhang
- China National Bamboo Research Center, Hangzhou, China
| | - Xule Zhang
- Zhejiang Institute of Subtropical Crops, Wenzhou, China
| | - Xiaohua Ma
- Zhejiang Institute of Subtropical Crops, Wenzhou, China
| | - Jian Zheng
- Zhejiang Institute of Subtropical Crops, Wenzhou, China
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Bhandari MS, Meena RK, Shamoon A, Saroj S, Kant R, Pandey S. First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora. Mol Biol Rep 2020; 47:6997-7008. [PMID: 32930932 DOI: 10.1007/s11033-020-05758-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022]
Abstract
Salvadoraceae constitutes ecologically imperative desert families of 3 genera-Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.
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Affiliation(s)
- Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India.
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shanti Saroj
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand, 248 006, India
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Jia B, Wang G, Zheng J, Yang W, Chang S, Zhang J, Liu Y, Li Q, Ge C, Chen G, Liu D, Yang F. Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer. Hereditas 2020; 157:24. [PMID: 32591015 PMCID: PMC7320565 DOI: 10.1186/s41065-020-00137-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler. RESULTS We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027. CONCLUSIONS This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.
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Affiliation(s)
- Boyin Jia
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Guiwu Wang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Junjun Zheng
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Wanyun Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Shuzhuo Chang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Jiali Zhang
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Qining Li
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Chenxia Ge
- College of Vocational and Technical Education, Changchun Sci-Tech University, 1699 Donghua Street, Changchun, 130606, China
| | - Guang Chen
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Dongdong Liu
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China. .,College of Engineering and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - Fuhe Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China.
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Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm ( Elaeis guineensis Jacq.). 3 Biotech 2020; 10:280. [PMID: 32537380 DOI: 10.1007/s13205-020-02269-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022] Open
Abstract
Present study mainly aimed to ascertain the distribution characteristics of gene-based microsatellite loci and to develop polymorphic SSR markers from the already available transcriptome data of Elaeis guineensis Jacq, an important oil crop. From this study, we identified the sum of 5791 SSRs across 51,425 unigenes from the transcripts of oil palm. We were able to evaluate 331primer pairs and characterized 183 polymorphic gene-based SSR markers. We identified a total of 506 alleles from the 183 polymorphic SSR loci, with an average of 2.77 alleles per locus. The characterized gene-based SSR markers from the transcriptome data of oil palm exhibited moderate levels of polymorphism with a significant level of heterozygosity ranges from 0.096 to 0.594 (mean = 0.336 ± 0.11). Among the identified SSR markers, sixty polymorphic markers were used to analyze genotypes of 55 oil palm accessions selected from three different provinces of China. Association mapping analysis provided the information of four markers that are associated with fruit shell thickness trait of oil palm. Among the four markers identified from association analysis, one SSR marker obtained from Unigene17150 is strictly associated with the oil palm fruit shell thickness trait.
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Hao DC, Xiao PG. Pharmaceutical resource discovery from traditional medicinal plants: Pharmacophylogeny and pharmacophylogenomics. CHINESE HERBAL MEDICINES 2020; 12:104-117. [PMID: 36119793 PMCID: PMC9476761 DOI: 10.1016/j.chmed.2020.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 01/25/2023] Open
Abstract
The worldwide botanical and medicinal culture diversity are astonishing and constitute a Pierian spring for innovative drug R&D. Here, the latest awareness and the perspectives of pharmacophylogeny and pharmacophylogenomics, as well as their expanding utility in botanical drug R&D, are systematically summarized and highlighted. Chemotaxonomy is based on the fact that closely related plants contain the same or similar chemical profiles. Correspondingly, it is better to combine morphological characters, DNA markers and chemical markers in the inference of medicinal plant phylogeny. Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic effects, thus forming the core of pharmacophylogeny. Here we systematically review and comment on the versatile applications of pharmacophylogeny in (1) looking for domestic resources of imported drugs, (2) expanding medicinal plant resources, (3) quality control, identification and expansion of herbal medicines, (4) predicting the chemical constituents or active ingredients of herbal medicine and assisting in the identification and determination of chemical constituents, (5) the search for new drugs sorting out, and (6) summarizing and improving herbal medicine experiences, etc. Such studies should be enhanced within the context of deeper investigations of molecular biology and genomics of traditional medicinal plants, phytometabolites and metabolomics, and ethnomedicine-based pharmacological activity, thus enabling the sustainable conservation and utilization of traditional medicinal resources.
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Affiliation(s)
- Da-cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China
- Corresponding author.
| | - Pei-gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
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Chai M, Ye H, Wang Z, Zhou Y, Wu J, Gao Y, Han W, Zang E, Zhang H, Ru W, Sun G, Wang Y. Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers. Front Genet 2020; 11:177. [PMID: 32194635 PMCID: PMC7065708 DOI: 10.3389/fgene.2020.00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.
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Affiliation(s)
- Min Chai
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hang Ye
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Yuancheng Zhou
- Triticeae Research Institute, Shanxi Academy of Agricultural Science, Linfen, China
| | - Jiahui Wu
- School of Life Sciences, Shanxi Normal University, Linfen, China.,Changzhi University, Changzhi, China
| | - Yue Gao
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Wei Han
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - En Zang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hao Zhang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, Canada
| | - Yling Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
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