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Mishra G, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta. Funct Integr Genomics 2023; 23:51. [PMID: 36707443 PMCID: PMC9883139 DOI: 10.1007/s10142-023-00975-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Abstract
Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.
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Affiliation(s)
- Garima Mishra
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun - 248 006, Uttarakhand, Dehradun, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India.
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Minh Nguyen D, Lan Phan Nguyen H, Minh Nguyen T. Genetic structure of the endemic Dipterocarpus condorensis revealed by microsatellite markers. AOB PLANTS 2022; 14:plac007. [PMID: 35440974 PMCID: PMC9011383 DOI: 10.1093/aobpla/plac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Anthropogenic disturbances in tropical forests often affect the genetic diversity of a species. Dipterocarpus condorensis is an endangered species in the tropical forests of south-eastern Vietnam, both from its over-exploitation and habitat loss. Therefore, knowledge of population genetic diversity and population structure is essential for identifying the species conservation measures. In the present study, we evaluated genetic diversity and population structure using nine microsatellites for 183 individual trees from eight populations, representing the distribution range of D. condorensis in Vietnam. Two clustering approaches (Bayesian analysis and discriminant analysis of principal components) revealed that all studied individuals clustered into three genetic groups, which were related to gene flow across the range of D. condorensis in the lowland tropical forests of south-eastern Vietnam. Limited gene flow was implicated in anthropogenic disturbance. Genetic differentiation among populations was relatively low (the Weir and Cockerham index of 0.122 and the Hedrick index of 0.149) and showed significant differentiation. The genetic variability of the populations was low (H O = 0.298 and H E = 0.324), which suggested the negative effects of habitat degradation and over-exploitation. Our studies also determined that D. condorensis populations can have undergone recent bottlenecks. We recommend conservation activities for this species based on these results.
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Affiliation(s)
- Duc Minh Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Hong Lan Phan Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Tam Minh Nguyen
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
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Nguyen TM, Vu DD, Dang HP, Bui XTT, Nguyen HPL, Nguyen DM. Population genetic structure and demographic history of the dipterocarp species Anisoptera costata Korth revealed by microsatellite analysis. PLANTA 2021; 253:66. [PMID: 33582857 DOI: 10.1007/s00425-021-03584-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Moderate levels of genetic diversity and differentiation of Anisoptera costata were determined. A population divergence occurred during Younger Dryas. The anthropogenic disturbance had significantly affected the genetic diversity of the species in low tropical forests. Anisoptera costata Korth, an endangered species, is mainly distributed in the lowland tropical forests of the Southeast region in Vietnam, which has not been explored for genetic diversity and demographic history. In this study, eight polymorphic microsatellite markers were used to analyze 232 wild trees of A. costata at nine different populations, representing the natural distribution range of the species in Vietnam. Genetic diversity within the populations was determined with mean values of 0.284 and 0.327 observed and expected heterozygosity, respectively, while genetic differentiation among populations was found with Weir and Cockerham index of 0.12 and Hedrick index of 1.38. These results indicated that habitat fragmentation by the anthropogenic disturbance may be the major factor for the low heterozygosity values and affected the number of alleles in all the targeted populations of A. costata in lowland tropical forests. Populations in the Central Southeast area had a higher level of genetic diversity than the populations in the Coastal and Western Southeast areas. The analysis of molecular variance showed that high genetic variation existed within populations (86.15%) compared to the variation among populations. A reduction in the population size of A. costata was determined by BOTTLENECK. Different clustering methods (Bayesian analysis, the neighbor-joining tree, and principal coordinate analysis) suggested optimal genetic clusters related to gene flow among different areas. Approximate Bayesian computation suggested that population divergence occurred during Younger Dryas. We also discussed the measures for species conservation based on these results.
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Affiliation(s)
- Tam Minh Nguyen
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.
| | - Duy Dinh Vu
- Vietnam-Russia Tropical Centre, Nguyen Van Huyen, Cau Giay, Hanoi, 100000, Vietnam
| | - Hien Phan Dang
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Xuan Thi Tuyet Bui
- Department of Plant Ecology, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Hong Phan Lan Nguyen
- Faculty of Biotechnology, Hanoi Open University, Nguyen Trai, Thanh Xuan, Hanoi, 100000, Vietnam
| | - Duc Minh Nguyen
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
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Cvetković T, Hinsinger DD, Strijk JS. Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing. Sci Rep 2019; 9:11639. [PMID: 31406227 PMCID: PMC6690942 DOI: 10.1038/s41598-019-48240-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/01/2019] [Indexed: 11/09/2022] Open
Abstract
Tropical forests, a key-category of land ecosystems, are faced with the world's highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae are one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae, and thus changes in habitat ecology, community composition and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genome. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinatus, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed low level of genomic diversity among analysed range-edge species, and different evolutionary history of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics and evolutionary studies.
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Affiliation(s)
- Tijana Cvetković
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China
| | - Damien Daniel Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000, Luang Prabang, Lao PDR
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, P.R. China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, 530005, P.R. China.
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000, Luang Prabang, Lao PDR.
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Gu X, Zhu JY, Jian KL, Wang BJ, Peng XR, Yang GY, Wang T, Zhong ZJ, Peng KY. Absence of population genetic structure in Heterakis gallinarum of chicken from Sichuan, inferred from mitochondrial cytochrome c oxidase subunit I gene. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3612-7. [PMID: 26394200 DOI: 10.3109/19401736.2015.1079825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Population genetics information provides a foundation for understanding the transmission and epidemiology of parasite and, therefore, may be used to assist in the control of parasitosis. However, limited available sequence information in Heterakis gallinarum has greatly impeded the study in this area. In this study, we first investigated the genetic variability and genetic structure of H. gallinarum. The 1325 bp fragments of the mitochondrial COX1 gene were amplified in 56 isolates of H. gallinarum from seven different geographical regions in Sichuan province, China. The 56 sequences were classified into 22 haplotypes (H1-H22). The values of haplotype diversity (0.712) and nucleotide diversity (0.00158) in Sichuan population indicate a rapid expansion occurred from a relatively small, short-term effective population in the past. The haplotype network formed a distribution around H1 in a star-like topology, and the haplotypes did not cluster according to their geographical location. Similar conclusions could be made from MP phylogenetic tree. The Fst value (Fst<0.16965) and AMOVA analysis revealed that no significant genetic differentiation was observed among the seven different geographical populations. Neutrality tests (Tajima's D and Fu's Fs) and mismatch analysis indicated that H. gallinarum experienced a population expansion in the past. Our results indicated that H. gallinarum experienced a rapid population expansion in the past, and there was a low genetic diversity and an absence of population structure across the population.
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Affiliation(s)
- Xiaobin Gu
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Jun-Yang Zhu
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Ke-Ling Jian
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Bao-Jian Wang
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Xue-Rong Peng
- b Department of Chemistry , College of Life and Basic Science, Sichuan Agricultural University , Ya'an , China , and
| | - Guang-You Yang
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Tao Wang
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Zhi-Jun Zhong
- a Department of Parasitology , College of Veterinary Medicine, Sichuan Agricultural University , Chengdu , China
| | - Ke-Yun Peng
- c Department of Science and Technology , Ganzi Institute of Scientific and Technological Information , Ganzi , China
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