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Ji HY, Ye C, Chen YQ, Li JW, Hidayat A, Miao JL, Li JH, Wu JY, Zhai JW, Lan SR, Jin XH. Phylogenomics and biogeographical diversification of Collabieae (Orchidaceae) and its implication in the reconstruction of the dynamic history of Asian evergreen broadleaved forests. Mol Phylogenet Evol 2024; 196:108084. [PMID: 38688440 DOI: 10.1016/j.ympev.2024.108084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/16/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera. The diversification of the nine clades of Collabieae might be associated with the uplift of the Himalayas during the Late Oligocene/Early Miocene. The enhanced East Asian summer monsoon in the Late Miocene may have promoted the rapid diversification of Collabieae at a sustained high diversification rate. The increased size of terrestrial pseudobulbs may be one of the drivers of Collabieae diversification. Our results suggest that the establishment and development of evergreen broadleaved forests facilitated the diversification of Collabieae.
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Affiliation(s)
- Hong-Yu Ji
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 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, China
| | - Chao Ye
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yan-Qiong Chen
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Arief Hidayat
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Jiang-Lin Miao
- 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
| | | | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), 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.
| | - 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.
| | - Xiao-Hua Jin
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; China National Botanical Garden, Beijing, China.
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Fadzly N, Zuharah WF, Jenn Ney JW. Can plants fool artificial intelligence? Using machine learning to compare between bee orchids and bees. Plant Signal Behav 2021; 16:1935605. [PMID: 34151732 PMCID: PMC8331003 DOI: 10.1080/15592324.2021.1935605] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Bee orchids have long been an excellent example of how dishonest signal works in plant-animal interaction. Many studies compared the flower structures that resemble female bees, leading toward pseudo-copulation of the male bees on the flower. Using Machine Learning, we tested whether nature is capable of besting artificial intelligence. A total of 2000 images of related bees, wasps, and Ophrys sp. were collected from the Google Image Repository. Unsuitable images were later filtered out manually, leaving a total of 995 images in the final selection. 80% of these images were used to build a supervised model using Logistic Regression, while the model accuracy was tested using 20% of the remaining images. Based on our results using Wolfram Mathematica, the Ophrys is not capable of fooling artificial intelligence. The accuracy, accuracy baseline, mean cross-entropy, Area Under ROC (receiver operating characteristic curve) curve (AUC) and the confusion matrix gave excellent image classification. However, we can now show the key points and highlights of the images and how the structures closely resemble actual bees using the SURF method. Rather than just a descriptive method, ML learning has enabled a more quantitative approach. Since this is a simple test, we encourage other scientists to adopt our approach using a larger dataset and better database samples.
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Affiliation(s)
- Nik Fadzly
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Wan Fatma Zuharah
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Jenny Wong Jenn Ney
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
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3
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Górniak M, Jakubska-Busse A, Ziętara MS. Genetic History of the Remnant Population of the Rare Orchid Cypripedium calceolus Based on Plastid and Nuclear rDNA. Genes (Basel) 2021; 12:genes12060940. [PMID: 34205392 PMCID: PMC8235785 DOI: 10.3390/genes12060940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
The lady’s slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic variability, and processes in small populations are therefore crucial for the species’ protection. Nowadays, in south-west Poland, it is only distributed in seven small remnant and isolated populations, which we examined. One nuclear (ITS rDNA) and two plastid (accD-psa1, trnL-F) markers were analyzed and compared globally in this study. Based on the nuclear marker, the most common ancestor of C. calceolus and Cypripedium shanxiense existed about 2 million years ago (95% HPD: 5.33–0.44) in Asia. The division of the C. calceolus population into the European and Asian lineages indicated by C/T polymorphism started about 0.5 million years ago (95% HPD: 1.8–0.01). The observed variation of plastid DNA, which arose during the Pleistocene glacial–interglacial cycles, is still diffuse in Poland. Its distribution is explained by the result of fragmentation or habitat loss due to human impact on the environment.
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Affiliation(s)
- Marcin Górniak
- Department of Molecular Evolution, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.G.), (M.S.Z.)
| | - Anna Jakubska-Busse
- Department of Botany, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
- Correspondence:
| | - Marek S. Ziętara
- Department of Molecular Evolution, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (M.G.), (M.S.Z.)
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Serna-Sánchez MA, Pérez-Escobar OA, Bogarín D, Torres-Jimenez MF, Alvarez-Yela AC, Arcila-Galvis JE, Hall CF, de Barros F, Pinheiro F, Dodsworth S, Chase MW, Antonelli A, Arias T. Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution. Sci Rep 2021; 11:6858. [PMID: 33767214 PMCID: PMC7994851 DOI: 10.1038/s41598-021-83664-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 09/18/2019] [Accepted: 12/30/2020] [Indexed: 11/29/2022] Open
Abstract
Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
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Affiliation(s)
- Maria Alejandra Serna-Sánchez
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
- Biodiversity, Evolution and Conservation, EAFIT University, Cra. 49, No. 7 sur 50, Medellín, Colombia
| | | | - Diego Bogarín
- Jardín Botánico Lankester, Universidad de Costa Rica, P. O. Box 302-7050, Cartago, Costa Rica
- Endless Forms Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - María Fernanda Torres-Jimenez
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Astrid Catalina Alvarez-Yela
- Centro de Bioinformática y Biología Computacional (BIOS), Ecoparque Los Yarumos Edificio BIOS, Manizales, Colombia
| | - Juliana E Arcila-Galvis
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
| | - Climbie F Hall
- Instituto de Botânica, Núcleo de Pesquisa Orquídario Do Estado, Postal 68041, São Paulo, SP, 04045-972, Brasil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquídario Do Estado, Postal 68041, São Paulo, SP, 04045-972, Brasil
| | - Fábio Pinheiro
- Instituto de Biologia, Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Alexandre Antonelli
- Royal Botanic Gardens Kew, London, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Tatiana Arias
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia.
- Centro de Bioinformática y Biología Computacional (BIOS), Ecoparque Los Yarumos Edificio BIOS, Manizales, Colombia.
- Tecnológico de Antioquia, Calle 78B NO. 72A - 220, Medellín, Colombia.
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Koene FM, Amano É, Smidt EDC, Ribas LLF. Asymbiotic germination and morphological studies of seeds of Atlantic Rainforest micro-orchids (Pleurothallidinae). PLoS One 2020; 15:e0243297. [PMID: 33315920 PMCID: PMC7735581 DOI: 10.1371/journal.pone.0243297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/19/2020] [Indexed: 11/18/2022] Open
Abstract
The morphological and morphometric characters of seeds belonging to 11 species of the subtribe Pleurothallidinae using light and scanning electron microscopy were studied to understand the in vitro germination process. Qualitative data (color, shape, ornamentation) and quantitative ones were also evaluated in seeds and embryos (length, width, volume and air space percentage between the integument and the embryo). The viability of the seeds was evaluated by in vitro germination in woody plant medium (WPM), and by analysis of the developmental stages of protocorms until seedling formation (two to 24 weeks). Morphometric data showed variations within the genus Acianthera and between species of different genera. The best germination and protocorm formation responses occurred with Acianthera prolifera (92%) and Acianthera ochreata (86%), with the formation of seedlings after 12 and 16 weeks of sowing, respectively. The seeds and embryos of A. prolifera and A. ochreata were larger (length, width, and volume) with a structural polarity that may have facilitated their germination comparing to others studied species. Other characteristics of A. prolifera seeds that may have contributed to these results include the presence of a thin testa without ornamentation and a suspensor. The protocorms of Anathalis obovata, Dryadella liliputiana, and Octomeria gracillis developed slowly in the WPM, not reaching the seedling stage in 24 weeks of cultivation. This morphological and morphometric study contributes to the understanding of asymbiotic germination of some micro-orchid species.
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Affiliation(s)
- Franciele Marx Koene
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Érika Amano
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eric de Camargo Smidt
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Luciana Lopes Fortes Ribas
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
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6
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Leal BSS, Brandão MM, Palma-Silva C, Pinheiro F. Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains. BMC Plant Biol 2020; 20:554. [PMID: 33302865 PMCID: PMC7731501 DOI: 10.1186/s12870-020-02757-x] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/25/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic differences, few studies have inferred the role of gene expression for adaptive divergence in Neotropical systems. In this study, we conduct genome-wide expression analysis alongside soil elemental analysis in sympatric and allopatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae), which occur in contrasting adjacent habitats in the Neotropical coastal plains. RESULTS These species were highly differentiated by their gene expression profiles, as determined by 18-21% of transcripts. Gene ontology (GO) terms associated with reproductive processes were enriched according to comparisons between species in both allopatric and sympatric populations. Species showed differential expression in genes linked to salt and waterlogging tolerance according to comparisons between species in sympatry, and biological processes related to environmental stimulus appeared as representative among those transcripts associated with edaphic characteristics in each sympatric zone. Hybrids, in their turn, were well differentiated from E. fulgens, but exhibited a similar gene expression profile to flooding-tolerant E. puniceolutem. When compared with parental species, hybrids showed no transcripts with additive pattern of expression and increased expression for almost all transgressive transcripts. CONCLUSIONS This study sheds light on general mechanisms promoting ecological differentiation and assortative mating, and suggests candidate genes, such as those encoding catalase and calcium-dependent protein kinase, underling adaptation to harsh edaphic conditions in the Neotropical coastal plains. Moreover, it demonstrates that differential gene expression plays a central role in determining ecologically-based phenotypic differences among co-occurring species and their hybrids.
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Affiliation(s)
| | - Marcelo Mendes Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
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Joffard N, Arnal V, Buatois B, Schatz B, Montgelard C. Floral scent evolution in the section Pseudophrys: pollinator-mediated selection or phylogenetic constraints? Plant Biol (Stuttg) 2020; 22:881-889. [PMID: 32130747 DOI: 10.1111/plb.13104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/27/2019] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
Sexually deceptive orchid species from the Mediterranean genus Ophrys usually interact with one or a few pollinator species by means of specific floral scents. In this study, we investigated the respective role of pollinator-mediated selection and phylogenetic constraints in the evolution of floral scents in the section Pseudophrys. We built a phylogenetic tree of 19 Pseudophrys species based on three nuclear loci; we gathered a dataset on their pollination interactions from the literature and from our own field data; and we extracted and analysed their floral scents using solid phase microextraction and gas chromatography-mass spectrometry. We then quantified the phylogenetic signal carried by floral scents and investigated the link between plant-pollinator interactions and floral scent composition using phylogenetic comparative methods. We confirmed the monophyly of the section Pseudophrys and demonstrated the existence of three main clades within this section. We found that floral scent composition is affected by both phylogenetic relationships among Ophrys species and pollination interactions, with some compounds (especially fatty acid esters) carrying a significant phylogenetic signal and some (especially alkenes and alkadienes) generating dissimilarities between closely related Pseudophrys pollinated by different insects. Our results show that in the section Pseudophrys, floral scents are shaped both by pollinator-mediated selection and by phylogenetic constraints, but that the relative importance of these two evolutionary forces differ among compound classes, probably reflecting distinct selective pressures imposed upon behaviourally active and non-active compounds.
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Affiliation(s)
- N Joffard
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier, France
| | - V Arnal
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier, France
| | - B Buatois
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier, France
| | - B Schatz
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier, France
| | - C Montgelard
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, Montpellier, France
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Li BJ, Zheng BQ, Wang JY, Tsai WC, Lu HC, Zou LH, Wan X, Zhang DY, Qiao HJ, Liu ZJ, Wang Y. New insight into the molecular mechanism of colour differentiation among floral segments in orchids. Commun Biol 2020; 3:89. [PMID: 32111943 PMCID: PMC7048853 DOI: 10.1038/s42003-020-0821-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
An unbalanced pigment distribution among the sepal and petal segments results in various colour patterns of orchid flowers. Here, we explored this type of mechanism of colour pattern formation in flowers of the Cattleya hybrid 'KOVA'. Our study showed that pigment accumulation displayed obvious spatiotemporal specificity in the flowers and was likely regulated by three R2R3-MYB transcription factors. Before flowering, RcPAP1 was specifically expressed in the epichile to activate the anthocyanin biosynthesis pathway, which caused substantial cyanin accumulation and resulted in a purple-red colour. After flowering, the expression of RcPAP2 resulted in a low level of cyanin accumulation in the perianths and a pale pink colour, whereas RcPCP1 was expressed only in the hypochile, where it promoted α-carotene and lutein accumulation and resulted in a yellow colour. Additionally, we propose that the spatiotemporal expression of different combinations of AP3- and AGL6-like genes might participate in KOVA flower colour pattern formation.
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Affiliation(s)
- Bai-Jun Li
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
| | - Bao-Qiang Zheng
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650, Guangzhou, China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, 701, Tainan City, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, 701, Tainan City, Taiwan
| | - Hsiang-Chia Lu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Long-Hai Zou
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 311300, Lin'an, China
| | - Xiao Wan
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
- Research & Development Center of Flower, Zhejiang Academy of Agricultural Sciences, 311202, Hangzhou, China
| | - Di-Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Hong-Juan Qiao
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, 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, 350002, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangzhou, China.
| | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China.
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9
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Smidt EDC, Páez MZ, Vieira LDN, Viruel J, de Baura VA, Balsanelli E, de Souza EM, Chase MW. Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae). PLoS One 2020; 15:e0227991. [PMID: 31990943 PMCID: PMC6986716 DOI: 10.1371/journal.pone.0227991] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/03/2020] [Indexed: 11/26/2022] Open
Abstract
This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.
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Affiliation(s)
| | - Michelle Zavala Páez
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, England, United Kingdom
| | - Valter Antônio de Baura
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, England, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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10
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Brandrud MK, Baar J, Lorenzo MT, Athanasiadis A, Bateman RM, Chase MW, Hedrén M, Paun O. Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae). Syst Biol 2020; 69:91-109. [PMID: 31127939 PMCID: PMC6902629 DOI: 10.1093/sysbio/syz035] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 10/19/2018] [Revised: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 12/04/2022] Open
Abstract
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.
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Affiliation(s)
- Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Maria T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Alexander Athanasiadis
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | | | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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11
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Zhang Y, Zhou T, Dai Z, Dai X, Li W, Cao M, Li C, Tsai WC, Wu X, Zhai J, Liu Z, Wu S. Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population. Int J Mol Sci 2019; 21:E247. [PMID: 31905846 PMCID: PMC6982098 DOI: 10.3390/ijms21010247] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/25/2019] [Accepted: 12/26/2019] [Indexed: 12/12/2022] Open
Abstract
Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants.
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Affiliation(s)
- Yiyi Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Tinghong Zhou
- Huanglong National Scenic Reserve, Songpan 623300, China;
| | - Zhongwu Dai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Xiaoyu Dai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Wei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Mengxia Cao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Chengru Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Wen-Chieh Tsai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan City 701, China
| | - Xiaoqian Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
| | - Shasha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Z.D.); (X.D.); (W.L.); (M.C.); (C.L.); (W.-C.T.); (X.W.); (J.Z.)
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12
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Fan XL, Chomicki G, Hao K, Liu Q, Xiong YZ, Renner SS, Gao JY, Huang SQ. Transitions between the Terrestrial and Epiphytic Habit Drove the Evolution of Seed-Aerodynamic Traits in Orchids. Am Nat 2019; 195:275-283. [PMID: 32017633 DOI: 10.1086/706905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Orchids are globally distributed, a feature often attributed to their tiny dustlike seeds. They were ancestrally terrestrial but in the Eocene expanded into tree canopies, with some lineages later returning to the ground, providing an evolutionarily replicated system. Because seeds are released closer to the ground in terrestrial species than in epiphytic ones, seed traits in terrestrials may have been under selective pressure to increase seed dispersal efficiency. In this study, we test the expectations that seed airspace-a trait known to increase seed flotation time in the air-is (i) larger in terrestrial lineages and (ii) has increased following secondary returns to a terrestrial habit. We quantified and scored 20 seed traits in 121 species and carried out phylogenetically informed analyses. Results strongly support both expectations, suggesting that aerodynamic traits even in dust seeds are under selection to increase dispersal ability, following shifts in average release heights correlated with changes in habit.
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13
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Raskoti BB, Ale R. Molecular phylogeny and morphology reveal a new epiphytic species of Habenaria (Orchidaceae; Orchideae; Orchidinae) from Nepal. PLoS One 2019; 14:e0223355. [PMID: 31644547 PMCID: PMC6808328 DOI: 10.1371/journal.pone.0223355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Habenaria is almost cosmopolitan in distribution having predominantly terrestrial orchids, however; a remarkable epiphytic species with some unique morphological characters was collected from Nepal. We conducted a molecular phylogeny of this unusual Habenaria species using nuclear (ITS) and chloroplast (matK, rbcl) DNA sequence regions to infer its systematic position. Our molecular analyses and morphological treatment recognized this newly collected plant as an undescribed species. This species is described here which is closely related to Habenaria plurifoliata but can be distinguished by having its multiple growing callus-shaped tuber, smaller stature with short stem, longer and wider oblanceolate leaves, peduncle with a foliaceous bract and only one sterile bract, lateral sepals oblong, obtuse, petal apex obtuse, lateral lobes of lip spreading upwards, spur not exceeding the ovary and pedicel.
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Affiliation(s)
- Bhakta Bahadur Raskoti
- Nature Research and Conservation Initiatives, Pokharathok, Arghakhanchi, Nepal
- Nepal Bioscience Research Laboratory, Banasthali, Kathmandu, Nepal
| | - Rita Ale
- Nature Research and Conservation Initiatives, Pokharathok, Arghakhanchi, Nepal
- Nepal Bioscience Research Laboratory, Banasthali, Kathmandu, Nepal
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14
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Bogarín D, Pérez-Escobar OA, Karremans AP, Fernández M, Kruizinga J, Pupulin F, Smets E, Gravendeel B. Phylogenetic comparative methods improve the selection of characters for generic delimitations in a hyperdiverse Neotropical orchid clade. Sci Rep 2019; 9:15098. [PMID: 31641165 PMCID: PMC6805863 DOI: 10.1038/s41598-019-51360-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 09/19/2019] [Indexed: 11/28/2022] Open
Abstract
Taxonomic delimitations are challenging because of the convergent and variable nature of phenotypic traits. This is evident in species-rich lineages, where the ancestral and derived states and their gains and losses are difficult to assess. Phylogenetic comparative methods help to evaluate the convergent evolution of a given morphological character, thus enabling the discovery of traits useful for classifications. In this study, we investigate the evolution of selected traits to test for their suitability for generic delimitations in the clade Lepanthes, one of the Neotropical species-richest groups. We evaluated every generic name proposed in the Lepanthes clade producing densely sampled phylogenies with Maximum Parsimony, Maximum Likelihood, and Bayesian approaches. Using Ancestral State Reconstructions, we then assessed 18 phenotypic characters that have been traditionally employed to diagnose genera. We propose the recognition of 14 genera based on solid morphological delimitations. Among the characters assessed, we identified 16 plesiomorphies, 12 homoplastic characters, and seven synapomorphies, the latter of which are reproductive features mostly related to the pollination by pseudocopulation and possibly correlated with rapid diversifications in Lepanthes. Furthermore, the ancestral states of some reproductive characters suggest that these traits are associated with pollination mechanisms alike promoting homoplasy. Our methodological approach enables the discovery of useful traits for generic delimitations in the Lepanthes clade and offers various other testable hypotheses on trait evolution for future research on Pleurothallidinae orchids because the phenotypic variation of some characters evaluated here also occurs in other diverse genera.
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Affiliation(s)
- Diego Bogarín
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica.
- Herbarium UCH, Universidad Autónoma de Chiriquí, David, Chiriquí, Panama.
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands.
| | - Oscar A Pérez-Escobar
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adam P Karremans
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
| | - Melania Fernández
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jaco Kruizinga
- Hortus botanicus, Leiden University, Leiden, The Netherlands
| | - Franco Pupulin
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, P.O. Box 302-7050, Costa Rica
- Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, USA
- Marie Selby Botanical Gardens, 811 South Palm Avenue, Sarasota, Florida, 34236, USA
| | - Erik Smets
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- KU Leuven, Ecology, Evolution and Biodiversity Conservation, Leuven, Belgium
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
- University of Applied Sciences Leiden, Faculty of Science and Technology, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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15
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He C, Teixeira da Silva JA, Wang H, Si C, Zhang M, Zhang X, Li M, Tan J, Duan J. Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis. Sci Rep 2019. [PMID: 31554868 DOI: 10.1038/s41598-019-49812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | | - Haobin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoming Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mingzhi Li
- Biodata Biotechnology Co. Ltd, Heifei, 230031, China
| | - Jianwen Tan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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16
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Lallemand F, Logacheva M, Le Clainche I, Bérard A, Zheleznaia E, May M, Jakalski M, Delannoy É, Le Paslier MC, Selosse MA. Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids. Genome Biol Evol 2019; 11:2457-2467. [PMID: 31396616 PMCID: PMC6733356 DOI: 10.1093/gbe/evz170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2019] [Indexed: 12/12/2022] Open
Abstract
Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic, and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including 9 mixotrophic species and covering all 6 Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared with autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.
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Affiliation(s)
- Félix Lallemand
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Maria Logacheva
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Isabelle Le Clainche
- Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, Evry, France
| | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, Evry, France
| | - Ekaterina Zheleznaia
- Peoples’ Friendship University of Russia, Timiryazev State Biological Museum, Moscow, Russia
| | - Michał May
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Poland
| | - Marcin Jakalski
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Poland
| | - Étienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Orsay, France
- Université Evry, Université Paris-Saclay, Orsay, France
| | | | - Marc-André Selosse
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Poland
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17
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Mitoma M, Kajino Y, Hayashi R, Endo M, Kubota S, Kanno A. Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae). Plant J 2019; 99:439-451. [PMID: 30924980 DOI: 10.1111/tpj.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/08/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata, 'Hishou', has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip-like organs. Here, we isolated four DEFICIENS-like and two AGL6-like genes from H. radiata, and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the 'Hishou' cultivar, except HrDEF-C3. The HrDEF-C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in 'Hishou'. Sequence analysis of the HrDEF-C3 loci revealed that the 'Hishou' genome harbored two types of HrDEF-C3 genes: one identical to wild-type HrDEF-C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between 'Hishou' and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the HrDEF-C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the HrDEF-C3 promoter, resulting in the ectopic expression of HrDEF-C3. As the expression of HrAGL6-C2 was limited to lateral sepals and lip, the overlapping expression of HrDEF-C3 and HrAGL6-C2 is likely to be responsible for the sepal to lip-like identity in the lateral sepals of the 'Hishou' cultivar.
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Affiliation(s)
- Mai Mitoma
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Yumi Kajino
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Risa Hayashi
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Miyako Endo
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Shosei Kubota
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
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18
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Chen Y, Chen Y, Feng X, Yang X, Zhang J, Qiu Z, He Y. Variety Identification of Orchids Using Fourier Transform Infrared Spectroscopy Combined with Stacked Sparse Auto-Encoder. Molecules 2019; 24:molecules24132506. [PMID: 31324007 PMCID: PMC6651824 DOI: 10.3390/molecules24132506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The feasibility of using the fourier transform infrared (FTIR) spectroscopic technique with a stacked sparse auto-encoder (SSAE) to identify orchid varieties was studied. Spectral data of 13 orchids varieties covering the spectral range of 4000-550 cm-1 were acquired to establish discriminant models and to select optimal spectral variables. K nearest neighbors (KNN), support vector machine (SVM), and SSAE models were built using full spectra. The SSAE model performed better than the KNN and SVM models and obtained a classification accuracy 99.4% in the calibration set and 97.9% in the prediction set. Then, three algorithms, principal component analysis loading (PCA-loading), competitive adaptive reweighted sampling (CARS), and stacked sparse auto-encoder guided backward (SSAE-GB), were used to select 39, 300, and 38 optimal wavenumbers, respectively. The KNN and SVM models were built based on optimal wavenumbers. Most of the optimal wavenumbers-based models performed slightly better than the all wavenumbers-based models. The performance of the SSAE-GB was better than the other two from the perspective of the accuracy of the discriminant models and the number of optimal wavenumbers. The results of this study showed that the FTIR spectroscopic technique combined with the SSAE algorithm could be adopted in the identification of the orchid varieties.
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Affiliation(s)
- Yunfeng Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou 310021, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Xufeng Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zhengjun Qiu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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Hsu CC, Su CJ, Jeng MF, Chen WH, Chen HH. A HORT1 Retrotransposon Insertion in the PeMYB11 Promoter Causes Harlequin/Black Flowers in Phalaenopsis Orchids. Plant Physiol 2019; 180:1535-1548. [PMID: 31088902 PMCID: PMC6752922 DOI: 10.1104/pp.19.00205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/29/2019] [Indexed: 05/09/2023]
Abstract
The harlequin/black flowers in Phalaenopsis orchids contain dark purple spots and various pigmentation patterns, which appeared as a new color in 1996. We analyzed this phenotype by microscopy, HPLC, gene functional characterization, genome structure analysis, and transient overexpression system to obtain a better understanding of the black color formation in Phalaenopsis orchids. Most mesophyll cells of harlequin flowers showed extremely high accumulation of anthocyanins as well as a high expression of Phalaenopsis equestris MYB11 (PeMYB11) as the major regulatory R2R3-MYB transcription factor for regulating the production of the black color. In addition, we analyzed the expression of basic helix-loop-helix factors, WD40 repeat proteins, and MYB27- and MYBx-like repressors for their association with the spot pattern formation. To understand the high expression of PeMYB11 in harlequin flowers, we isolated the promoter sequences of PeMYB11 from red and harlequin flowers. A retrotransposon, named Harlequin Orchid RetroTransposon 1 (HORT1), was identified and inserted in the upstream regulatory region of PeMYB11 The insertion resulted in strong expression of PeMYB11 and thus extremely high accumulation of anthocyanins in the harlequin flowers of the Phalaenopsis Yushan Little Pearl variety. A dual luciferase assay showed that the insertion of HORT1 enhanced PeMYB11 expression by at least 2-fold compared with plants not carrying the insertion. Furthermore, the presence of HORT1 explains the high mutation rates resulting in many variations of pigmentation patterning in harlequin flowers of Phalaenopsis orchids.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Ching-Jen Su
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Mei-Fen Jeng
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
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Acemi A, Çobanoğlu Ö, Türker-Kaya S. FTIR-based comparative analysis of glucomannan contents in some tuberous orchids, and effects of pre-processing on glucomannan measurement. J Sci Food Agric 2019; 99:3681-3686. [PMID: 30638265 DOI: 10.1002/jsfa.9596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/12/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Glucomannan (GM) is a polysaccharide of the mannan family of compounds found in some plant species. The dried and powdered tubers of some orchid species, collectively known as 'salep powder,' are a commercially important crop for human consumption and are one of the primary sources of GM. GM content is the primary indicator for the yield and quality of salep powder. We hypothesized that it would be more practical and accurate to measure GM content within tuber powder directly, prior to any purification or pre-processing. The GM content of tubers of 14 different orchid species was evaluated and compared using Fourier transform infrared (FTIR) spectroscopy and an enzymatic colorimetric method. RESULTS Among the analyzed modes, the sum of the peak areas at 873 and 812 cm-1 , which represent the CH bending attributed to the β-pyranose form of d-glucose and d-mannose, respectively, gave the only confirmation using colorimetric methods. It was found that the tubers of Himantoglossum caprinum and Serapias vomeracea had the highest GM concentrations among the analyzed species. After conducting different pre-processing steps on Serapias vomeracea tubers, it was found that treating the tubers with milk, or high temperature resulted in an apparent increase in GM concentrations. CONCLUSION Himantoglossum caprinum and Serapias vomeracea give the highest yields of GM and should be used for commercial horticulture. GM estimation should be made prior to any pre-processing. FTIR spectroscopy is effective and reliable for directly comparing GM content of different orchid species, without the need for any purification or pre-processing. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Arda Acemi
- Department of Biology, Faculty of Arts and Sciences, Kocaeli University, Kocaeli, Turkey
| | - Özmen Çobanoğlu
- Department of Biology, Faculty of Arts and Sciences, Kocaeli University, Kocaeli, Turkey
| | - Sevgi Türker-Kaya
- Department of Biology, Faculty of Arts and Sciences, Kocaeli University, Kocaeli, Turkey
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Şenel G, Akbulut MK, Süngü Şeker Ş. Comparative anatomical properties of some Epidendroideae and Orchidoideae species distributed in NE Turkey. Protoplasma 2019; 256:655-668. [PMID: 30402736 DOI: 10.1007/s00709-018-1326-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/27/2017] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
In this research, anatomical, leaf micromorphological features of the samples belonging to 25 taxa (Anacamptis Rich., Cephalanthera Rich., Dactylorhiza Necker ex Nevski, Gymnadenia R.Br., Himantoglossum Spreng., Limodorum Boehm., Ophrys L., Orchis L., Platanthera Rich., Serapias L., Spiranthes Rich. and Steveniella Schltr.) spread in the Karadeniz Region have been evaluated comparatively. In anatomical studies, the transverse section from root, stem and leaf, and surface section from leaves of plants were examined. In addition, micromorphological properties of leaf were determined by electron microscopy. Morphometrical analyses were carried out using the anatomical and leaf micromophological characters of each taxa. The data matrices were obtained by examining the results of at least three samples collected from different localities. The data were evaluated using Statistical Package for the Social Sciences (SPSS) and PAleontological STatistics (PAST) statistical programs with PCA, linear discriminant analysis (LDA), and unweighted pair group method with arithmetic mean analysis. Anatomical characteristics of plants such as root epidermis cell length, cortex diameter and pith cell diameter, leaf upper epidermis length-width and bulliform cell length-width were determined to be important characteristics. It was concluded that these characters are especially important in grouping at the genus level.
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de Almeida ABR, Smidt EDC, Amano E. Evolution of anatomical characters in Acianthera section Pleurobotryae (Orchidaceae: Pleurothallidinae). PLoS One 2019; 14:e0212677. [PMID: 30865720 PMCID: PMC6415883 DOI: 10.1371/journal.pone.0212677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/07/2019] [Indexed: 11/25/2022] Open
Abstract
Acianthera section Pleurobotryae is one of ten sections of the genus Acianthera and include four species endemic to the Atlantic Forest. The objective of this study was to describe comparatively the anatomy of vegetative organs and floral micromorphology of all species of Acianthera section Pleurobotryae in order to identify diagnostic characters between them and synapomorphies for the section in relation of other sections of the genus. We analyzed roots, ramicauls, leaves and flowers of 15 species, covering eight of the nine sections of Acianthera, using light microscopy and scanning electron microscopy. Acianthera section Pleurobotryae is a monophyletic group and the cladistic analyses of anatomical and flower micromorphology data, combined with molecular data, support internal relationship hypotheses among the representatives of this section. The synapomorphies identified for A. sect. Pleurobotryae are based on leaf anatomy: unifacial leaves, round or elliptical in cross-section, round leaves with vascular bundles organized in concentric circles, and mesophyll with 28 to 30 cell layers. Within the section, the clade (A. crepiniana + A. mantiquyrana) presented more differences in vegetative organ morphology and higher support values in combined analyses when compared to the second clade, (A. atropurpurea + A. hatschbachii). For each of these clades an exclusive set of homoplasies of vegetative and floral organs were also identified. The results support the argument that vegetative organs are more evolutionarily stable in comparison to reproductive organs and thus helpful for inference of internal phylogenetic relationships in Acianthera, while flowers are highly variable, perhaps due to the diversity of pollinator attraction mechanisms. The analyses indicate that the elliptical leaves observed in A. crepiniana have originated from round leaves observed in the other species of this section, suggesting an adaptation to increase the area of exposure of the leaf and better the efficiency of capture of sunlight in shaded environments such as the Atlantic Forest. The presence of papillose regions in both vegetative and floral organs indicated that micromorphological characters are also useful for the delimitation of species and sections within the genus.
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Affiliation(s)
| | - Eric de Camargo Smidt
- Programa de Pós-Graduação em Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Erika Amano
- Programa de Pós-Graduação em Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
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23
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Abstract
BACKGROUND The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. RESULTS In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. CONCLUSIONS Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.
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Affiliation(s)
- Zhang-Hai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yun-Xia Li
- Fujian Agriculture and Forest University, Shanxiadian Road 15, Changshan District, Fuzhou, 350002, Fujian, China
| | - Cheng-Wang Wang
- Nanchang University, Xuefu Road 999, Honggutang District, Nanchang, Jiangxi, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Nay Pyi Taw, Myanmar.
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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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Roma L, Cozzolino S, Schlüter PM, Scopece G, Cafasso D. The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids. PLoS One 2018; 13:e0204174. [PMID: 30226857 PMCID: PMC6143245 DOI: 10.1371/journal.pone.0204174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022] Open
Abstract
Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus.
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Affiliation(s)
- Luca Roma
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Salvatore Cozzolino
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- * E-mail:
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
- Institute of Botany, University of Hohenheim, Garbenstraße 30, Stuttgart, Germany
| | - Giovanni Scopece
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Donata Cafasso
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
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Dong WL, Wang RN, Zhang NY, Fan WB, Fang MF, Li ZH. Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution. Int J Mol Sci 2018; 19:ijms19030716. [PMID: 29498674 PMCID: PMC5877577 DOI: 10.3390/ijms19030716] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.
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Affiliation(s)
- Wan-Lin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Na-Yao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wei-Bing Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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Jin WT, Schuiteman A, Chase MW, Li JW, Chung SW, Hsu TC, Jin XH. Phylogenetics of subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation. BMC Plant Biol 2017; 17:222. [PMID: 29178835 PMCID: PMC5702240 DOI: 10.1186/s12870-017-1160-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/08/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Subtribe Orchidinae (Orchidaceae, Orchidoideae) are a nearly cosmopolitan taxon of terrestrial orchids, comprising about 1800 species in 47 to 60 genera. Although much progress has been made in recent years of phylogenetics of Orchidinae, considerable problems remain to be addressed. Based on molecular phylogenetics, we attempt to illustrate the phylogenetic relationships and discuss generic delimitation within Orchidinae. Seven DNA markers (five plastid and two nuclear), a broad sampling of Orchidinae (400 species in 52 genera) and three methods of phylogenetic analysis (maximum likelihood, maximum parsimony and Bayesian inference) were used. RESULTS Orchidinae s.l. are monophyletic. Satyrium is sister to the rest of Orchidinae s.l. Brachycorythis and Schizochilus are successive sister to Asian-European Orchidinae s.s. Sirindhornia and Shizhenia are successive sister to clade formed by Tsaiorchis-Hemipilia-Ponerorchis alliance. Stenoglottis is sister to the Habenaria-Herminium-Peristylus alliance. Habenaria, currently the largest genus in Orchidinae, is polyphyletic and split into two distant clades: one Asian-Australian and the other African-American-Asian. Diplomeris is sister to Herminium s.l. plus Asian-Australian Habenaria. CONCLUSIONS We propose to recognize five genera in the Ponerorchis alliance: Hemipilia, Ponerorchis s.l., Sirindhornia, Shizhenia and Tsaiorchis. Splitting Habenaria into two genera based on morphological characters and geographical distribution may be the least disruptive approach, and it is reasonable to keep Satyrium in Orchidinae.
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Affiliation(s)
- Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 10093 China
| | - André Schuiteman
- Identification and Naming Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB UK
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS UK
- School of Plant Biology, University of Western Australia, Crawley, Perth, 6009 Australia
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan 666303 China
| | - Shih-Wen Chung
- Botanical Garden Division, Taiwan Forestry Research Institute, 53 Nanhai Road, Taipei, Taiwan 10066 China
| | - Tian-Chuan Hsu
- Department of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan 30013 China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 10093 China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Yezin, Nay Pyi Taw, Myanmar
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Kim HT, Chase MW. Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae). PLoS One 2017; 12:e0187318. [PMID: 29140976 PMCID: PMC5695243 DOI: 10.1371/journal.pone.0187318] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/17/2017] [Indexed: 11/23/2022] Open
Abstract
In this paper, we compare ndh genes in the plastid genome of many Cymbidium species and three closely related taxa in Orchidaceae looking for evidence of ndh gene degradation. Among the 11 ndh genes, there were frequently large deletions in directly repeated or AT-rich regions. Variation in these degraded ndh genes occurs between individual plants, apparently at population levels in these Cymbidium species. It is likely that ndh gene transfers from the plastome to mitochondrial genome (chondriome) occurred independently in Orchidaceae and that ndh genes in the chondriome were also relatively recently transferred between distantly related species in Orchidaceae. Four variants of the ycf1-rpl32 region, which normally includes the ndhF genes in the plastome, were identified, and some Cymbidium species contained at least two copies of that region in their organellar genomes. The four ycf1-rpl32 variants seem to have a clear pattern of close relationships. Patterns of ndh degradation between closely related taxa and translocation of ndh genes to the chondriome in Cymbidium suggest that there have been multiple bidirectional intracellular gene transfers between two organellar genomes, which have produced different levels of ndh gene degradation among even closely related species.
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Affiliation(s)
- Hyoung Tae Kim
- College of Agriculture and Life Sciences, Kyungpook University, Daegu, Korea
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
- * E-mail:
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Pérez-Escobar OA, Gottschling M, Chomicki G, Condamine FL, Klitgård BB, Pansarin E, Gerlach G. Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics. Sci Rep 2017; 7:4919. [PMID: 28687774 PMCID: PMC5501825 DOI: 10.1038/s41598-017-04261-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/22/2017] [Indexed: 11/17/2022] Open
Abstract
The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany.
- Identification and Naming department, Royal Botanic Gardens, Kew, TW9 3AB, Surrey, UK.
| | - Marc Gottschling
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany
| | - Guillaume Chomicki
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut de Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Bente B Klitgård
- Identification and Naming department, Royal Botanic Gardens, Kew, TW9 3AB, Surrey, UK
| | - Emerson Pansarin
- Departamento de Biologia, Facultade de Filosofia, Ciências e Letras, Universidade de Sao Paulo, Ribeirao Preto, SP, 14040-901, Brazil
| | - Günter Gerlach
- Botanischer Garten München, Menzinger Straße 61, D - 80638, Munich, Germany.
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Ahrens CW, Supple MA, Aitken NC, Cantrill DJ, Borevitz JO, James EA. Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain. Ann Bot 2017; 119:1267-1277. [PMID: 28334284 PMCID: PMC5604565 DOI: 10.1093/aob/mcx022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 01/21/2017] [Accepted: 02/12/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. METHODS Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. KEY RESULTS Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation. CONCLUSIONS Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units.
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Affiliation(s)
- Collin W. Ahrens
- Royal Botanic Gardens Victoria, Science Division, Melbourne, Victoria 3004, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- For correspondence. E-mail
| | - Megan A. Supple
- Australian National University, Research School of Biology, Centre of Excellence in Plant Energy Biology, Canberra, ACT 0200, Australia
| | - Nicola C. Aitken
- Australian National University, Research School of Biology, Centre of Excellence in Plant Energy Biology, Canberra, ACT 0200, Australia
| | - David J. Cantrill
- Royal Botanic Gardens Victoria, Science Division, Melbourne, Victoria 3004, Australia
| | - Justin O. Borevitz
- Australian National University, Research School of Biology, Centre of Excellence in Plant Energy Biology, Canberra, ACT 0200, Australia
| | - Elizabeth A. James
- Royal Botanic Gardens Victoria, Science Division, Melbourne, Victoria 3004, Australia
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Kowalkowska AK, Turzyński S, Kozieradzka-Kiszkurno M, Wiśniewska N. Floral structure of two species of Bulbophyllum section Cirrhopetalum Lindl.: B. weberi Ames and B. cumingii (Lindl.) Rchb. f. (Bulbophyllinae Schltr., Orchidaceae). Protoplasma 2017; 254:1431-1449. [PMID: 27798718 PMCID: PMC5376396 DOI: 10.1007/s00709-016-1034-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 10/10/2016] [Indexed: 05/25/2023]
Abstract
Flowers of Bulbophyllum weberi and B. cumingii are characterized by fly-pollinated features. The secretory activity was described in dorsal sepals in both species (putative osmophores), petals in B. weberi (possible osmophores) and adaxial surface of lips in both species. In the cells of dorsal sepals and petals of B. weberi proteins, dihydroxyphenols, lipids and starch grains were detected, in lateral sepals-lipids. Whereas in dorsal sepal of B. cumingii only lipids and starch grains were noted, in lateral sepals-proteins and dihydroxyphenols and in petals-proteins and starch grains. The lips in both species differed histochemically and ultrastructurally. The epidermal cells of lip groove in B. weberi contained lipids, proteins, starch grains in cytoplasm, dihydroxyphenols in vacuoles and pectic acids/mucilage on surface. Whereas in B. cumingii-few lipids, starch grains, no proteins, no dihydroxyphenols and no mucilage were noted. Ultrastructurally, in B. weberi, the secretory material was present on surface and vesicles building into plasmalemma, while in B. cumingii-cell wall ingrowths and microchannels in cuticle. The osmiophilic irregular materials and globular, osmiophilic globules in B. weberi are probably tannin-like materials. For the first time, we described the cell wall ingrowths in Bulbophyllum species: in lip of B. cumingii and petals of B. weberi.
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Affiliation(s)
- Agnieszka K Kowalkowska
- Department of Plant Cytology and Embryology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Sławomir Turzyński
- Department of Plant Cytology and Embryology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | | | - Natalia Wiśniewska
- Department of Plant Cytology and Embryology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
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Cevallos S, Sánchez-Rodríguez A, Decock C, Declerck S, Suárez JP. Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids? Mycorrhiza 2017; 27:225-232. [PMID: 27882467 DOI: 10.1007/s00572-016-0746-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 06/18/2016] [Accepted: 11/15/2016] [Indexed: 05/20/2023]
Abstract
In epiphytic orchids, distinctive groups of fungi are involved in the symbiotic association. However, little is known about the factors that determine the mycorrhizal community structure. Here, we analyzed the orchid mycorrhizal fungi communities associated with three sympatric Cymbidieae epiphytic tropical orchids (Cyrtochilum flexuosum, Cyrtochilum myanthum, and Maxillaria calantha) at two sites located within the mountain rainforest of southern Ecuador. To characterize these communities at each orchid population, the ITS2 region was analyzed by Illumina MiSeq technology. Fifty-five mycorrhizal fungi operational taxonomic units (OTUs) putatively attributed to members of Serendipitaceae, Ceratobasidiaceae and Tulasnellaceae were identified. Significant differences in mycorrhizal communities were detected between the three sympatric orchid species as well as among sites/populations. Interestingly, some mycorrhizal OTUs overlapped among orchid populations. Our results suggested that populations of studied epiphytic orchids have site-adjusted mycorrhizal communities structured around keystone fungal species. Interaction with multiple mycorrhizal fungi could favor orchid site occurrence and co-existence among several orchid species.
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Affiliation(s)
- Stefania Cevallos
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 2, box L7.05.06, B-1348, Louvain-la-Neuve, Belgium
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, 11-01-608, Loja, Ecuador
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, 11-01-608, Loja, Ecuador
| | - Cony Decock
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Mycothèque de l'Université catholique de Louvain (MUCL1), Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 2, box L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, 11-01-608, Loja, Ecuador.
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Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0-A Transcriptomics Resource for the Orchid Family. Plant Cell Physiol 2017; 58:e9. [PMID: 28111366 DOI: 10.1093/pcp/pcw220] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 09/22/2016] [Accepted: 12/01/2016] [Indexed: 05/18/2023]
Abstract
Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2.0 has been built with a new database system to store the annotations of 510,947 protein-coding genes and 161,826 noncoding transcripts, covering 18 orchid species belonging to 12 genera in five subfamilies of Orchidaceae. We have improved the N50 size of protein-coding genes, provided new functional annotations (including protein-coding gene annotations, protein domain/family information, pathways analysis, Gene Ontology term assignments, orthologous genes across orchid species, cross-links to the database of model species, and miRNA information), and improved the user interface with better website performance. We also provide new database functionalities for database searching and sequence retrieval. Moreover, the Orchidstra 2.0 database incorporates detailed RNA-Seq gene expression data from various tissues and developmental stages in different orchid species. The database will be useful for gene prediction and gene family studies, and for exploring gene expression in orchid species. The Orchidstra 2.0 database is freely accessible at http://orchidstra2.abrc.sinica.edu.tw.
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Affiliation(s)
- Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shao-Hua Yen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jen-Hau Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJD, Clements MA, Arroyo MTK, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, Cameron KM. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proc Biol Sci 2016; 282:rspb.2015.1553. [PMID: 26311671 DOI: 10.1098/rspb.2015.1553] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.
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Pedersen HÆ, Srimuang KO, Watthana S. Strengthening the taxonomic backbone of Thai orchid conservation: genetic fingerprinting and morphometry applied to a species complex in Geodorum. Ann Bot 2016; 118:125-33. [PMID: 27192705 PMCID: PMC4934394 DOI: 10.1093/aob/mcw071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/02/2015] [Revised: 01/18/2016] [Accepted: 03/28/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS A well-supported classification is crucial for conservation planning, but intricate species complexes constitute a serious challenge to the preparation of flora accounts. In preparation of the Flora of Thailand account on Geodorum (Orchidaceae), it was decided to use multivariate morphometric analysis and genetic fingerprinting to resolve the intricate G. pulchellum sensu Seidenfaden/G. siamense species complex, with the specific aim of testing the taxonomic soundness of the apparently rare and conservation-requiring G. pulchellum sensu Seidenfaden. Geodorum densiflorum, universally considered distinct from the above species complex, was included as reference. METHODS Morphometric data and tissue samples for amplified fragment length polymorphism (AFLP) analysis were collected from 17 Geodorum populations in northern and north-eastern Thailand. Principal components analysis was employed to summarize the patterns of phenetic variation. Hierarchical genetic differentiation between populations was explored using Bayesian inference followed by cluster analysis. KEY RESULTS The taxonomic distinction of G. densiflorum was generally supported. In contrast, G. siamense and G. pulchellum sensu Seidenfaden were poorly separated, especially according to the estimated patterns of inter-population genetic differentiation. CONCLUSIONS The G. pulchellum sensu Seidenfaden/G. siamense complex should be treated as one variable species (under the name G. siamense), meaning that G. pulchellum sensu Seidenfaden should not be given high independent conservation priority. This study demonstrates that flora accounts can benefit from prior employment of multivariate and Bayesian methods for exploring intricate species complexes, in turn leading to more solid decisions and priorities in a conservation context.
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Affiliation(s)
- Henrik Æ Pedersen
- Biosystematics, Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 2C, DK-1353 Copenhagen K, Denmark
| | - Kanok-Orn Srimuang
- School of Agriculture and Natural Resources, University of Phayao, 19 M. 2 T. Mae-ka, Muang District, Phayao 56000, Thailand
| | - Santi Watthana
- Queen Sirikit Botanic Garden, PO Box 7, Mae Rim, Chiang Mai 50180, Thailand
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Liu WL, Shih HC, Weng IS, Ko YZ, Tsai CC, Chou CH, Chiang YC. Characterization of Genomic Inheritance of Intergeneric Hybrids between Ascocenda and Phalaenopsis Cultivars by GISH, PCR-RFLP and RFLP. PLoS One 2016; 11:e0153512. [PMID: 27055268 PMCID: PMC4824505 DOI: 10.1371/journal.pone.0153512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/30/2016] [Indexed: 11/18/2022] Open
Abstract
Background The intergeneric hybrids between Ascocenda John De Biase ‘Blue’ and Phalaenopsis Chih Shang's Stripes have been generated to introduce the blue color into the Phalaenopsis germplasm in prior study. In order to confirm the inheritance in hybrid progenies, genomic in situ hybridization (GISH) and restriction fragment length polymorphism (RFLP) analysis were conducted to confirm the intergeneric hybridization status. Methods/Results GISH analysis showed the presence of both maternal and paternal chromosomes in the cells of the putative hybrids indicating that the putative hybrid seedlings were intergeneric hybrids of the two parents. Furthermore, twenty-seven putative hybrids were randomly selected for DNA analysis, and the external transcribed spacer (ETS) regions of nrDNA were analyzed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and RFLP analyses to identify the putative hybrids. RFLP analysis showed that the examined seedlings were intergeneric hybrids of the two parents. However, PCR-RFLP analysis showed bias to maternal genotype. Conclusions Both GISH and RFLP analyses are effective detection technology to identify the intergeneric hybridization status of putative hybrids. Furthermore, the use of PCR-RFLP analysis to identify the inheritance of putative hybrids should be carefully evaluated.
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Affiliation(s)
- Wen-Lin Liu
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Huei-Chuan Shih
- Department of Nursing, Meiho University, Pingtung 912, Taiwan
| | - I-Szu Weng
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Chi-Chu Tsai
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
- National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung 404, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
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Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity (Edinb) 2016; 116:351-61. [PMID: 26604189 PMCID: PMC4787024 DOI: 10.1038/hdy.2015.98] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
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Affiliation(s)
- F Balao
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Tannhäuser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Hedrén
- Department of Biology, Lund University, Lund, Sweden
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Zhang L, Chen F, Zhang GQ, Zhang YQ, Niu S, Xiong JS, Lin Z, Cheng ZMM, Liu ZJ. Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. Plant J 2016; 86:175-85. [PMID: 26959080 DOI: 10.1111/tpj.13159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 10/23/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 05/20/2023]
Abstract
Crassulacean acid metabolism (CAM) is a CO2 fixation pathway that maximizes water-use efficiency (WUE), compared with the C3/C4 CO2 pathway, which permits CAM plants to adapt to arid environments. The CAM pathway provides excellent opportunities to genetically design plants, especially bioenergy crops, with a high WUE and better photosynthetic performance than C3/C4 in arid environments. The information available on the origin and evolution of CAM is scant, however. Here, we analyzed transcriptomes from 13 orchid species and two existing orchid genomes, covering CAM and C3 plants, with an emphasis on comparing 13 gene families involved in the complete carbon fixation pathway. The dosage of the core photosynthesis-related genes plays no substantial role in the evolution of CAM in orchids; however, CAM may have evolved primarily by changes at the transcription level of key carbon fixation pathway genes. We proposed that in both dark and light, CO2 is primarily fixed and then released through two metabolic pathways via known genes, such as PPC1, PPDK and PPCK. This study reports a comprehensive comparison of carbon fixation pathway genes across different photosynthetic plants, and reveals the importance of the level of expression of key genes in the origin and evolution of CAM.
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Affiliation(s)
- Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Shance Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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Ponert J, Trávníček P, Vuong TB, Rybková R, Suda J. A New Species of Cleisostoma (Orchidaceae) from the Hon Ba Nature Reserve in Vietnam: A Multidisciplinary Assessment. PLoS One 2016; 11:e0150631. [PMID: 27008538 PMCID: PMC4805174 DOI: 10.1371/journal.pone.0150631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/16/2016] [Indexed: 11/22/2022] Open
Abstract
A new species, Cleisostoma yersinii J. Ponert & Vuong, is described and illustrated based on the material collected in the Hon Ba Nature Reserve in southern Vietnam. In addition to conventional (macro)morphological examination we comparatively investigated root and leaf anatomy (using light and fluorescent microscopy), assessed nectar characteristics (using HPLC analysis), determined nuclear genome size (using DNA flow cytometry) and reconstructed phylogenetic relationships (using nrITS sequences). Cleisostoma yersinii differs from its putative closest relative C. birmanicum in wider and shorter leaves, larger flowers, distinct lip with S-shaped tip of the mid-lobe, and a shallow spur with two large nectar sacks separated by prominent calli and septum. Nectar is sucrose-dominant and very rich in sugars. Stomata are developed on both sides of the leaf and have prominent hyperstomatal chambers and substomatal cavities. Roots with well-developed exodermis and tracheoidal idioblasts are covered by a two-layer Vanda-type velamen. Chloroplasts occur not only in the cortex but are also abundant in the stele. Mean 1C-value was estimated to 2.57 pg DNA. An updated identification key is provided for SE Asian sections and all Vietnamese species of Cleisostoma.
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Affiliation(s)
- Jan Ponert
- Prague Botanical Garden, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| | - Pavel Trávníček
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Truong Ba Vuong
- Institute of Tropical Biology, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | | | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
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Gamisch A, Fischer GA, Comes HP. Frequent but asymmetric niche shifts in Bulbophyllum orchids support environmental and climatic instability in Madagascar over Quaternary time scales. BMC Evol Biol 2016; 16:14. [PMID: 26781289 PMCID: PMC4717530 DOI: 10.1186/s12862-016-0586-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 07/20/2015] [Accepted: 01/12/2016] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Species or clades may retain or shift their environmental niche space over evolutionary time. Understanding these processes offers insights into the environmental processes fuelling lineage diversification and might also provide information on past range dynamics of ecosystems. However, little is known about the relative contributions of niche conservatism versus niche divergence to species diversification in the tropics. Here, we examined broad-scale patterns of niche evolution within a Pliocene-Pleistocene clade of epiphytic Bulbophyllum orchids (30 spp.) whose collective distribution covers the northwest and eastern forest ecosystems of Madagascar. RESULTS Using species occurrence data, ecological niche models, and multivariate analyses of contributing variables, we identified a three-state niche distribution character for the entire clade, coinciding with three major forest biomes viz. phytogeographical provinces in Madagascar: A, Northwest 'Sambirano'; B, 'Eastern Lowlands'; and C, 'Central Highlands'. A time-calibrated phylogeny and Bayesian models of niche evolution were then used to detect general trends in the direction of niche change over the clade's history (≤5.3 Ma). We found highest transitions rates between lowlands (A and B) and (mostly from B) into the highland (C), with extremely low rates out of the latter. Lowland-to-highland transitions occurred frequently during the Quaternary, suggesting that climate-induced vegetational shifts promoted niche transitions and ecological speciation at this time. CONCLUSIONS Our results reveal that niche transitions occurred frequently and asymmetrically within this Madagascan orchid clade, and in particular over Quaternary time scales. Intrinsic features germane to Bulbophyllum (e.g., high dispersal ability, drought tolerance, multiple photosynthetic pathways) as well as extrinsic factors (ecological, historical) likely interacted to generate the niche transition patterns observed. In sum, our results support the emerging idea of dramatic environmental and climatic fluctuations in Madagascar during the recent geological past, which overturns the long-held paradigm of long-term stability in tropical forest settings. The generality of the patterns and timings reported here awaits the availability of additional comparative studies in other Madagascan endemics.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
| | | | - Hans Peter Comes
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
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Kim HT, Kim JS, Moore MJ, Neubig KM, Williams NH, Whitten WM, Kim JH. Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries. PLoS One 2015; 10:e0142215. [PMID: 26558895 PMCID: PMC4641739 DOI: 10.1371/journal.pone.0142215] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/19/2015] [Indexed: 12/26/2022] Open
Abstract
Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Jung Sung Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Michael J. Moore
- Department of Biology, Oberlin College, Oberlin, Ohio, United States of America
| | - Kurt M. Neubig
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Norris H. Williams
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - W. Mark Whitten
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015. [PMID: 26416561 DOI: 10.1186/s12862-015-0491-491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015; 15:210. [PMID: 26416561 PMCID: PMC4587860 DOI: 10.1186/s12862-015-0491-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/20/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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Gamisch A, Fischer GA, Comes HP. Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end. BMC Evol Biol 2015; 15:192. [PMID: 26376901 PMCID: PMC4574068 DOI: 10.1186/s12862-015-0471-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/28/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The transition from outcrossing to selfing has long been portrayed as an 'evolutionary dead end' because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a 'rostellum') co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing. RESULTS The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.4-3.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. ≤ 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing. CONCLUSIONS The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the 'rostellum') is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary (≤ 1.3 Ma) time scales.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
| | | | - Hans Peter Comes
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
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Ospina-Torres R, Montoya-Pfeiffer PM, Parra-H A, Solarte V, Tupac Otero J. Interaction networks and the use of floral resources by male orchid bees (Hymenoptera: Apidae: Euglossini) in a primary rain forests of the Chocó Region (Colombia). REV BIOL TROP 2015; 63:647-658. [PMID: 26666122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Orchid bees are important keystone pollinators from the Neotropics. With the aim to study the relationships between orchid bees and their nectar and aromatic host species, we made systematic samplings of males across two conservation areas in the biogeographic Choc6 Region of Colombia. We used chemical baits to collect 352 male bees during five months. The pollen attached to their bodies was extracted for palynological identification and to estimate interaction networks. The euglossine community consisted of at least 22 species including Eg. maculilabris, Eg. orellana, Eg. championi and Eg. ignita. The male bees were associated with 84 plants but depended on a small group of them (Peperomia spp. and Anthurium spp, as well as species of Solanaceae, Ericaceae and Malpighiaceae) which were widely distributed across the altitudinal gradient, and were available through the year. The resulting interaction networks revealed a typical nested pattern usually found in plant-pollinator interactions, with several rare bee and plant species interaction with a small group of generalist bees and plant species. Albeit, we found variation within networks related to species composition. Such variation may be a consequence of specific differences in plant flowering phenology.
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Zhao D, Zhou T, Jiang WK, Xiao CH, Kang CZ. [Identification of Bletillae Rhizoma and its adulterants by SNPs in ITS2]. Zhongguo Zhong Yao Za Zhi 2015; 40:3573-3578. [PMID: 26983202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To establish a molecular identification method for Bletillae Rhizoma, this paper extracted genome DNA from Bletillae Rhizoma and its adulterants. The sequences of rDNA ITS2 were sequenced after amplifying. Then multiple alignments of ITS2 were constructed phylogenetic tree with Neighbor Joining by MEGA 5. 1 and found out SNPs loci. The result showed that rDNA ITS2 region could identify Bletillae Rhizoma and its adulterants. There existed the SNPs loci, which could identify Bletilla striata and B. ochracea. Furthermore, we designed specific primers against the SNPs loci of B. striata and B. ochracea, then screened primers and optimized the PCR amplification conditions. Finally, the DNA of B. striata and B. ochracea were specifically amplified by BJ59-412F, BJ59-412R and HHBJ-225R. The length of amplification products were respectively about 350 bp and 520 bp that were effectively identified of B. striata and B. ochracea. While, the adulterants of Bletillae Rhizoma were no-reaction occurring. To sum up, the amplification conditions of the primers can identify B. striata, B. ochracea and their adulterants successfully at the same time. This method was easy, time-saving, and reliable, which can be used as a rapid method for molecular identification of Bletillae Rhizoma.
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Li L, Ye DP, Niu M, Yan HF, Wen TL, Li SJ. Thuniopsis: A New Orchid Genus and Phylogeny of the Tribe Arethuseae (Orchidaceae). PLoS One 2015; 10:e0132777. [PMID: 26244769 PMCID: PMC4526666 DOI: 10.1371/journal.pone.0132777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/16/2015] [Indexed: 11/24/2022] Open
Abstract
An investigation of a questionable orchid led to the discovery of a new genus and species Thuniopsis cleistogama, endemic to Yunnan province, China. It is characterized by having a subglobose corm, a spike-like (racemose) inflorescence, half opened and spurless flowers, a collar-shaped stigma and subglobose capsules. Based on DNA sequence data from three gene regions (nuclear ribosomal ITS, chloroplast matK and trnL), we investigated its phylogenetic position within the tribe Arethuseae. Phylogenies using maximum likelihood and Bayesian inference support the recognition of Thuniopsis as a distinct genus, and suggest its close relationship to the genera Bletilla, Dilochia, and Thunia. The new genus is circumscribed and a description and illustrations of the new species are provided. The phylogenetic relationships among the genera in Arethuseae are accessed. Moreover, our phylogeny also shed light on the phylogenetic positions of several genera which, to date, remain uncertain.
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Affiliation(s)
- Lin Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
| | - De-Ping Ye
- Forest Bureau of Pu’er, Yunnan, P. R. China
| | - Miao Niu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
| | - Tie-Long Wen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
| | - Shi-Jin Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
- * E-mail:
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Abstract
Specklinia dunstervillei is described as a new species in recognition of the distinctness of a Venezuelan species related to and confused with Specklinia endotrachys. It was illustrated for the first time by G. C. K. Dunsterville in 1963 from a plant collected in Trujillo on the Cordillera de Merida. The newly named species can be easily recognized by its small habit, short leaves and small reddish-orange flowers, the non-ascending dorsal sepal and the obtuse petals that are shortly apiculate. Specklinia dunstervillei is formally described and illustrated once again and compared morphologically and genetically with its closest relatives.
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Affiliation(s)
- Adam P. Karremans
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302–7050, Cartago, Costa Rica
- Naturalis Biodiversity Center, Leiden University, Leiden, The Netherlands
- * E-mail:
| | - Franco Pupulin
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302–7050, Cartago, Costa Rica
- Harvard University Herbaria, Cambridge, Massachusetts, United States of America, and Marie Selby Botanical Gardens, Sarasota, Florida, United States of America
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden University, Leiden, The Netherlands
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Tang Y, Yukawa T, Bateman RM, Jiang H, Peng H. Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers. BMC Evol Biol 2015; 15:96. [PMID: 26006185 PMCID: PMC4479074 DOI: 10.1186/s12862-015-0376-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/08/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae plus an in-depth analysis of 110 representative accessions, encompassing most widely recognized species within the alliance, to elucidate their relationships. RESULTS We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (nrITS, low-copy Xdh) and four chloroplast (matK, psbA-trnH, trnL-F, trnS-trnG) markers. Nuclear and plastid data were analyzed separately due to a few hard incongruences that most likely reflect chloroplast capture. Our results suggest key phylogenetic placements for Sirindhornia and Brachycorythis, and confirm previous assertions that the Amitostigma alliance is monophyletic and sister to the Eurasian plus European clades of subtribe Orchidinae. Seven robust clades are evident within the alliance, but none corresponds precisely with any of the traditional genera; the smaller and more morphologically distinct genera Tsaiorchis, Hemipilia, Neottianthe and Hemipiliopsis are monophyletic but each is nested within a polyphyletic plexus of species attributed to either Ponerorchis or the most plesiomorphic genus, Amitostigma. Two early-divergent clades that escaped analysis by Jin et al. undermine their attempt to circumscribe an expanded monophyletic genus Ponerorchis. CONCLUSIONS We provide a new framework on the complex phylogenetic relationships between Amitostigma and other genera traditionally included in its alliance; based on which, we combine the entire Amitostigma alliance into a morphologically and molecularly circumscribed Amitostigma sensu latissimo that also contains seven molecularly circumscribed sections. Our molecular trees imply unusually high levels of morphological homoplasy, but these will need to be quantified via a future group-wide review of the alliance based on living plants if morphology is to be fully integrated into our classification.
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Affiliation(s)
- Ying Tang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tomohisa Yukawa
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.
| | - Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK.
| | - Hong Jiang
- Yunnan Academy of Forestry/Yunnan Laboratory for Conservation of Rare, Endangered and Endemic Forest Plants, State Forestry Administration, Kunming, 650204, Yunnan, China.
| | - Hua Peng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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