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Ning HJ, Gui FF, Tian EW, Yang LY. The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium. BMC PLANT BIOLOGY 2023; 23:492. [PMID: 37833649 PMCID: PMC10571305 DOI: 10.1186/s12870-023-04499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis. RESULT In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses. CONCLUSION In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.
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Affiliation(s)
- Hui-Juan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Fang-Fang Gui
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - En-Wei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Li-Yuan Yang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou, 311300, Zhejiang, China.
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Zhang G, Hu Y, Huang MZ, Huang WC, Liu DK, Zhang D, Hu H, Downing JL, Liu ZJ, Ma H. Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1204-1225. [PMID: 36738233 DOI: 10.1111/jipb.13462] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/03/2023] [Indexed: 05/13/2023]
Abstract
Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29 Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.
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Affiliation(s)
- Guojin Zhang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ming-Zhong 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
| | - Wei-Chang Huang
- Shanghai Chenshan Botanical Garden, Songjiang, Shanghai, 201602, China
| | - Ding-Kun 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
| | - Diyang Zhang
- 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
| | - Haihua Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jason L Downing
- Fairchild Tropical Botanic Garden, Coral Gables, Florida, 33156, USA
| | - 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
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- 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
| | - Xue-Wei Zhao
- 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
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan 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
| | - Shi-Jie Ke
- 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
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, 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 350002, 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
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:406-421. [PMID: 35510493 DOI: 10.1111/tpj.15799] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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5
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Zhang JY, Liao M, Cheng YH, Feng Y, Ju WB, Deng HN, Li X, Plenković-Moraj A, Xu B. Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:911702. [PMID: 35812969 PMCID: PMC9257239 DOI: 10.3389/fpls.2022.911702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773-207,142 bp in length and contained 128-130 genes, including 82-84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species.
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Affiliation(s)
- Jun-Yi Zhang
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Min Liao
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Cheng
- Wolong National Natural Reserve Administration Bureau, Sichuan, China
| | - Yu Feng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wen-Bing Ju
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Heng-Ning Deng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiong Li
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Bo Xu
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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6
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Wong DCJ, Peakall R. Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond. FRONTIERS IN PLANT SCIENCE 2022; 13:910362. [PMID: 35712597 PMCID: PMC9196242 DOI: 10.3389/fpls.2022.910362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 06/10/2023]
Abstract
The Orchidaceae is rivaled only by the Asteraceae as the largest plant family, with the estimated number of species exceeding 25,000 and encompassing more than 700 genera. To gain insights into the mechanisms driving species diversity across both global and local scales, well-supported phylogenies targeting different taxonomic groups and/or geographical regions will be crucial. High-throughput sequencing technologies have revolutionized the field of molecular phylogenetics by simplifying the process of obtaining genome-scale sequence data. Consequently, there has been an explosive growth of such data in public repositories. Here we took advantage of this unprecedented access to transcriptome data from predominantly non-phylogenetic studies to assess if it can be repurposed to gain rapid and accurate phylogenetic insights across the orchids. Exhaustive searches revealed transcriptomic data for more than 100 orchid species spanning 5 subfamilies, 13 tribes, 21 subtribes, and 50 genera that were amendable for exploratory phylotranscriptomic analysis. Next, we performed re-assembly of the transcriptomes before strategic selection of the final samples based on a gene completeness evaluation. Drawing on these data, we report phylogenetic analyses at both deep and shallow evolutionary scales via maximum likelihood and shortcut coalescent species tree methods. In this perspective, we discuss some key outcomes of this study and conclude by highlighting other complementary, albeit rarely explored, insights beyond phylogenetic analysis that repurposed multi-tissue transcriptome can offer.
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Phylotranscriptomic and Evolutionary Analyses of Oedogoniales (Chlorophyceae, Chlorophyta). DIVERSITY 2022. [DOI: 10.3390/d14030157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study determined the transcriptomes of eight Oedogoniales species, including six species from Oedogonium and two species from Oedocladium to conduct phylotranscriptomic and evolutionary analyses. 155,952 gene families and 192 single-copy orthogroups were detected. Phylotranscriptomic analyses based on single-copy orthogroups were conducted using supermatrix and coalescent-based approaches. The phylotranscriptomic analysis results revealed that Oedogonium is polyphyletic, and Oedocladium clustered with Oedogonium. Together with the transcriptomes of the OCC clade in the public database, the phylogenetic relationship of the three orders (Oedogoniales, Chaetophorales, Chaetopeltidales) is discussed. The non-synonymous (dN) to synonymous substitution (dS) ratios of single-copy orthogroups of the terrestrial Oedogoniales species using a branch model of phylogenetic analysis by maximum likelihood were estimated, which showed that 92 single-copy orthogroups were putative rapidly evolving genes. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses results revealed that some of the rapidly evolving genes were associated with photosynthesis, implying that terrestrial Oedogoniales species experienced rapid evolution to adapt to terrestrial habitats. The phylogenetic results combined with evolutionary analyses suggest that the terrestrialization process of Oedogoniales may have occured more than once.
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Peakall R, Wong DCJ, Phillips RD, Ruibal M, Eyles R, Rodriguez-Delgado C, Linde CC. A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids. Mol Ecol Resour 2021; 21:1118-1140. [PMID: 33453072 DOI: 10.1111/1755-0998.13327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 11/30/2022]
Abstract
With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference-guided assembly, before target sequence extraction, annotation and alignment, and application of a homology-aware k-mer block phylogenomic approach, prior to maximum likelihood and coalescence-based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 samples spanning the tribe, and 72 samples involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1-5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k-mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.
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Affiliation(s)
- Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia
| | - Monica Ruibal
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rodney Eyles
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Claudia Rodriguez-Delgado
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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10
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Piñeiro Fernández L, Byers KJR.P, Cai J, Sedeek KEM, Kellenberger RT, Russo A, Qi W, Aquino Fournier C, Schlüter PM. A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia. FRONTIERS IN PLANT SCIENCE 2019; 10:1553. [PMID: 31850034 PMCID: PMC6895147 DOI: 10.3389/fpls.2019.01553] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/07/2019] [Indexed: 05/30/2023]
Abstract
The orchids (Orchidaceae) constitute one of the largest and most diverse families of flowering plants. They have evolved a great variety of adaptations to achieve pollination by a diverse group of pollinators. Many orchids reward their pollinators, typically with nectar, but the family is also well-known for employing deceptive pollination strategies in which there is no reward for the pollinator, in the most extreme case by mimicking sexual signals of pollinators. In the European flora, two examples of these different pollination strategies are the sexually deceptive genus Ophrys and the rewarding genus Gymnadenia, which differ in their level of pollinator specialization; Ophrys is typically pollinated by pseudo-copulation of males of a single insect species, whilst Gymnadenia attracts a broad range of floral visitors. Here, we present and describe the annotated floral transcriptome of Ophrys iricolor, an Andrena-pollinated representative of the genus Ophrys that is widespread throughout the Aegean. Furthermore, we present additional floral transcriptomes of both sexually deceptive and rewarding orchids, specifically the deceptive Ophrys insectifera, Ophrys aymoninii, and an updated floral transcriptome of Ophrys sphegodes, as well as the floral transcriptomes of the rewarding orchids Gymnadenia conopsea, Gymnadenia densiflora, Gymnadenia odoratissima, and Gymnadenia rhellicani (syn. Nigritella rhellicani). Comparisons of these novel floral transcriptomes reveal few annotation differences between deceptive and rewarding orchids. Since together, these transcriptomes provide a representative sample of the genus-wide taxonomic diversity within Ophrys and Gymnadenia (Orchidoideae: Orchidinae), we employ a phylogenomic approach to address open questions of phylogenetic relationships within the genera. Specifically, this includes the controversial placement of O. insectifera within the Ophrys phylogeny and the placement of "Nigritella"-type morphologies within the phylogeny of Gymnadenia. Whereas in Gymnadenia, several conflicting topologies are supported by a similar number of gene trees, a majority of Ophrys gene topologies clearly supports a placement of O. insectifera as sister to a clade containing O. sphegodes.
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Affiliation(s)
- Laura Piñeiro Fernández
- Institute of Botany, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Kelsey J. R .P. Byers
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Jing Cai
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Khalid E. M. Sedeek
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Centre, Giza, Egypt
| | - Roman T. Kellenberger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alessia Russo
- Institute of Botany, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Centre Zurich, Zurich, Switzerland
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11
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Li YX, Li ZH, Schuiteman A, Chase MW, Li JW, Huang WC, Hidayat A, Wu SS, Jin XH. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Mol Phylogenet Evol 2019; 139:106540. [DOI: 10.1016/j.ympev.2019.106540] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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12
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Wong DCJ, Amarasinghe R, Falara V, Pichersky E, Peakall R. Duplication and selection in β-ketoacyl-ACP synthase gene lineages in the sexually deceptive Chiloglottis (Orchidaceace). ANNALS OF BOTANY 2019; 123:1053-1066. [PMID: 30789664 PMCID: PMC6589519 DOI: 10.1093/aob/mcz013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/05/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS The processes of gene duplication, followed by divergence and selection, probably underpin the evolution of floral volatiles crucial to plant-insect interactions. The Australian sexually deceptive Chiloglottis orchids use a class of 2,5-dialkylcyclohexan-1,3-dione volatiles or 'chiloglottones' to attract specific male wasp pollinators. Here, we explore the expression and evolution of fatty acid pathway genes implicated in chiloglottone biosynthesis. METHODS Both Chiloglottis seminuda and C. trapeziformis produce chiloglottone 1, but only the phylogenetically distinct C. seminuda produces this volatile from both the labellum callus and glandular sepal tips. Transcriptome sequencing and tissue-specific contrasts of the active and non-active floral tissues was performed. The effects of the fatty acid synthase inhibitor cerulenin on chiloglottone production were tested. Patterns of selection and gene evolution were investigated for fatty acid pathway genes. KEY RESULTS Tissue-specific differential expression of fatty acid pathway transcripts was evident between active and non-active floral tissues. Cerulenin significantly inhibits chiloglottone 1 production in the active tissues of C. seminuda. Phylogenetic analysis of plant β-ketoacyl synthase I (KASI), a protein involved in fatty acid biosynthesis, revealed two distinct clades, one of which is unique to the Orchidaceae (KASI-2B). Selection analysis indicated a strong signal of positive selection at the split of KASI-2B followed by relaxed purifying selection in the Chiloglottis clade. CONCLUSIONS By capitalizing on a phylogenetically distinct Chiloglottis from earlier studies, we show that the transcriptional and biochemical dynamics linked to chiloglottone biosynthesis in active tissues are conserved across Chiloglottis. A combination of tissue-specific expression and relaxed purifying selection operating at specific fatty acid pathway genes may hold the key to the evolution of chiloglottones.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
- For correspondence. E-mail ,
| | - Ranamalie Amarasinghe
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - Vasiliki Falara
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
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13
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
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14
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Luo D, Li Y, Zhao Q, Zhao L, Ludwig A, Peng Z. Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers. Genes (Basel) 2019; 10:E38. [PMID: 30634684 PMCID: PMC6356338 DOI: 10.3390/genes10010038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called "living fossil" species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
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Affiliation(s)
- Dehuai Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Lianpeng Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
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Majeed A, Singh A, Choudhary S, Bhardwaj P. RNAseq‐based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae. Cladistics 2018; 35:461-468. [PMID: 34633712 DOI: 10.1111/cla.12362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Aasim Majeed
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Amandeep Singh
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Shruti Choudhary
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
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16
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Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC. Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:631-640. [PMID: 29608785 DOI: 10.1002/ajb2.1047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
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Affiliation(s)
- Sarah A Unruh
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung 404, Taiwan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Science Museum, Amakubo, Tsukuba, 305-0005, Japan
| | | | - Richard P Shefferson
- Organization for Programs on Environmental Sciences, University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Ann Smithson
- Smithson Environmental Consultancy & DNALabs Environmental Genetics Testing, Bassendean, Western Australia, 6054
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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17
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Bateman RM, Sramkó G, Paun O. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids. ANNALS OF BOTANY 2018; 121:85-105. [PMID: 29325077 PMCID: PMC5786241 DOI: 10.1093/aob/mcx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/02/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. METHODS At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. KEY RESULTS RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. CONCLUSIONS The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.
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Affiliation(s)
- Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
- For correspondence. E-mail
| | - Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Egyetem, Debrecen, Hungary
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg, Vienna, Austria
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D. Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. METABARCODING AND METAGENOMICS 2017. [DOI: 10.3897/mbmg.1.19862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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