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Nanjala C, Wanga VO, Odago W, Mutinda ES, Waswa EN, Oulo MA, Mkala EM, Kuja J, Yang JX, Dong X, Hu GW, Wang QF. Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis. BMC Plant Biol 2022; 22:387. [DOI: https:/doi.org/10.1186/s12870-022-03736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/29/2022] [Indexed: 06/21/2023]
Abstract
Abstract
Background
Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.
Results
The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.
Conclusion
This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.
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Nanjala C, Wanga VO, Odago W, Mutinda ES, Waswa EN, Oulo MA, Mkala EM, Kuja J, Yang JX, Dong X, Hu GW, Wang QF. Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis. BMC Plant Biol 2022; 22:387. [PMID: 35918646 PMCID: PMC9347164 DOI: 10.1186/s12870-022-03736-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/29/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae. RESULTS The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius. CONCLUSION This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.
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Affiliation(s)
- Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Wyclif Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
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Zhang GQ, Chen GZ, Chen LJ, Zhai JW, Huang J, Wu XY, Li MH, Peng DH, Rao WH, Liu ZJ, Lan SR. Phylogenetic incongruence in Cymbidium orchids. Plant Divers 2021; 43:452-461. [PMID: 35024514 PMCID: PMC8720702 DOI: 10.1016/j.pld.2021.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 06/14/2023]
Abstract
Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution.
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Affiliation(s)
- Guo-Qiang Zhang
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Hui Rao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Si-Ren Lan
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Abstract
•The project, Orchid Diversity Survey in China, has been initiated by Department of Wildlife Conservation of National Forestry and Grassland Administration (DWC-NFGA) from 2019 to 2022.•During botanical investigation, approximately 30 new species and 10 newly recorded species have been discovered.
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Affiliation(s)
- Zhihua Zhou
- Department of Wildlife Conservation, National Forestry and Grassland Administration, No. 18, Hepingli Dongjie, Beijing 100714, China
| | - Ronghong Shi
- Department of Wildlife Conservation, National Forestry and Grassland Administration, No. 18, Hepingli Dongjie, Beijing 100714, China
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Chen Y, Zhong H, Zhu Y, Huang Y, Wu S, Liu Z, Lan S, Zhai J. Plastome structure and adaptive evolution of Calanthe s.l. species. PeerJ 2020; 8:e10051. [PMID: 33083127 PMCID: PMC7566753 DOI: 10.7717/peerj.10051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022] Open
Abstract
Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.
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Affiliation(s)
- Yanqiong Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hui Zhong
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yating Zhu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuanzhen Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shasha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Yang BY, Luo HL, Huang WC, Xiong DJ, Tan SL, Li B. Calanthe sieboldopsis (Orchidaceae, Epidendroideae, Collabieae), a new species from Luoxiao Mountains, eastern China. PhytoKeys 2020; 145:37-45. [PMID: 32327924 PMCID: PMC7165192 DOI: 10.3897/phytokeys.145.49386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
Calanthe sieboldopsis, a new species, is here described and illustrated from Luoxiao Mountains, Jiangxi Province, eastern China. It is morphologically similar to C. sieboldii Decne. ex Regel, but differs from the latter in having smaller flowers, longer spurs, rectangular mid-lobes with emarginate apex (vs. elliptic mid-lobes with mucronate apex), disc with 3 ridges and the proximal ends of the lateral 2 ridges enlarged with light reddish spots and minute white hairs (vs. disc with 5 ridges and 2 rows of white short hairs at base) and pollinia equal in size (vs. unequal in size). A preliminary risk-of-extinction assessment, according to the IUCN Red List Categories and Criteria, is given for the new species.
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Affiliation(s)
- Bo-Yun Yang
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Key Laboratory of Plant Resources in Jiangxi Province, Nanchang, Jiangxi 330031, China
| | - Huo-Lin Luo
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Key Laboratory of Plant Resources in Jiangxi Province, Nanchang, Jiangxi 330031, China
| | - Wei-Chang Huang
- Shanghai Chenshan Botanic Garden, Songjiang District, Shanghai 201602, China
| | - Dong-Jin Xiong
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Key Laboratory of Plant Resources in Jiangxi Province, Nanchang, Jiangxi 330031, China
| | - Shao-Lin Tan
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Key Laboratory of Plant Resources in Jiangxi Province, Nanchang, Jiangxi 330031, China
| | - Bo Li
- Research Centre of Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
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Chen YQ, Lan SR, Liu ZJ, Zhai JW. The complete chloroplast genome sequence of Calanthe delavayi (Orchidaceae), an endemic to China. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1601513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yan-Qiong Chen
- Key Laboratory of National Forestry and Grassland, Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fuzhou, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland, Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland, Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fuzhou, China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland, Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Fuzhou, China
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Hu C, Yang H, Jiang K, Wang L, Yang B, Hsieh T, Lan S, Huang W. Development of polymorphic microsatellite markers by using de novo transcriptome assembly of Calanthe masuca and C. sinica (Orchidaceae). BMC Genomics 2018; 19:800. [PMID: 30400862 PMCID: PMC6219035 DOI: 10.1186/s12864-018-5161-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/11/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest China. Both play important roles in horticulture and are under the pressure of population decline. Understanding their genetic background can greatly help us develop effective conservation strategies for these species. Simple sequence repeats (SSRs) are useful for genetic diversity analysis, presumably providing key information for the study and preservation of the wild populations of the two species we are interested in. RESULTS In this study, we performed RNA-seq analysis on the leaves of C. masuca and C. sinica, obtaining 40,916 and 71,618 unigenes for each species, respectively. In total, 2,019/3,865 primer pairs were successfully designed from 3,764/7,189 putative SSRs, among which 197 polymorphic SSRs were screened out according to orthologous gene pairs. After mononucleotide exclusion, a subset of 129 SSR primers were analysed, and 13 of them were found to have high polymorphism levels. Further analysis demonstrated that they were feasible and effective against C. masuca and C. sinica as well as transferable to another species in Calanthe. Molecular evolutionary analysis revealed functional pathways commonly enriched in unigenes with similar evolutionary rates in the two species, as well as pathways specific to each species, implicating species-specific adaptation. The divergence time between the two closely related species was tentatively determined to be 3.42 ± 1.86 Mya. CONCLUSIONS We completed and analysed the transcriptomes of C. masuca and C. sinica, assembling large numbers of unigenes and generating effective polymorphic SSR markers. This is the first report of the development of expressed sequence tag (EST)-SSR markers for Calanthe. In addition, our study could enable further genetic diversity analysis and functional and comparative genomic studies on Calanthe.
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Affiliation(s)
- Chao Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hongxing Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Kai Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Ling Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Boyun Yang
- School of Life Science, Nanchang University, Nanchang, 330031 China
| | - Tungyu Hsieh
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Siren Lan
- College of Landscape, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weichang Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- College of Landscape, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Park MS, Eimes JA, Oh SH, Suh HJ, Oh SY, Lee S, Park KH, Kwon HJ, Kim SY, Lim YW. Diversity of fungi associated with roots of Calanthe orchid species in Korea. J Microbiol 2018; 56:49-55. [PMID: 29299843 DOI: 10.1007/s12275-018-7319-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 01/08/2023]
Abstract
While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - John A Eimes
- University College, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sang Hoon Oh
- Department of Biology, Deajeon University, Daejeon, 34520, Republic of Korea
| | - Hwa Jung Suh
- Department of Biology, Deajeon University, Daejeon, 34520, Republic of Korea
| | - Seung-Yoon Oh
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seobihn Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki Hyeong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyuk Joon Kwon
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Soo-Young Kim
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea.
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Li Y, Tong Y, Xing F. DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China. Front Plant Sci 2016; 7:1791. [PMID: 27994608 PMCID: PMC5136562 DOI: 10.3389/fpls.2016.01791] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.
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Affiliation(s)
- Yuling Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yi Tong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
| | - Fuwu Xing
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Fuwu Xing
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