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Chen YY, Li C, Hsiao YY, Ho SY, Zhang ZB, Liao CC, Lee BR, Lin ST, Wu WL, Wang JS, Zhang D, Liu KW, Liu DK, Zhao XW, Li YY, Ke SJ, Zhou Z, Huang MZ, Wu YS, Peng DH, Lan SR, Chen HH, Liu ZJ, Wu WS, Tsai WC. OrchidBase 5.0: updates of the orchid genome knowledgebase. BMC Plant Biol 2022; 22:557. [PMID: 36456919 PMCID: PMC9717476 DOI: 10.1186/s12870-022-03955-5] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.
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Affiliation(s)
- You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chung‐I Li
- Department of Statistics, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Sau-Yee Ho
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhe-Bin Zhang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chien-Chi Liao
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Bing-Ru Lee
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shao-Ting Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Jeen-Shing Wang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Diyang Zhang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
| | - Ding-Kun Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xue-Wei Zhao
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yuan-Yuan Li
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Shi-Jie Ke
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Zhuang Zhou
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
| | - Ming-Zhong Huang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yong-Shu Wu
- Education Botanical Garden of Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Dong-Hui Peng
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Si-Ren Lan
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Hong-Hwa Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhong-Jian Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Lin DL, Ya JD, Schuiteman A, Ma CB, Liu C, Guo XL, Chen SS, Wang XL, Zhang ZR, Yu WB, Jin XH. Four new species and a new record of Orchidinae (Orchidaceae: Orchideae) from China. Plant Divers 2021; 43:390-400. [PMID: 34816064 PMCID: PMC8591144 DOI: 10.1016/j.pld.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 06/13/2023]
Abstract
Four new species of Orchidaceae from China, Heminium lijiangense, Peristylus fasciculatus, Platanthera milinensis, and Ponerorchis gongshanensis, together with a new country record, Peristylus tenuicallus, are described and illustrated based on morphological and/or phylogenetic analyses. Heminium lijiangense is closely related to H. elisabethae but differs from it by having the dorsal sepal ovate-orbicular and lip mid-lobe distinctly shorter than lateral lobes. P. fasciculatus is close to Peristylus tradescantifolius but is distinguished from it by having several fascicled and straight, root-like tubers (vs. one or two oblongoid tubers), old stems usually persistent, middle lobe of lip narrowly ligulate-lanceolate and half as long as the lateral lobes (vs. middle lobe deltoid, about a third as long as the lateral lobes or less), a raised callus at the base of each lateral lobe (vs. callus absent), spur gradually attenuate toward the apex (vs. spur clavate). Platanthera milinensis is similar to P. stenochila by sharing small green flowers and lip without a spur, but differs in having a creeping rhizome, a corymbose inflorescence, and a broadly ovate and slightly 3-lobed lip. Ponerochis gongshanensis is similar to P. faberi in its small flowers, but differs in having a linear leaf c. 3 mm wide (vs. leaf 5-13 mm wide), in the lip having collar-like raised margins on the sides of the spur entrance, and a mid-lobe which is notched at the apex but not divided into two divergent lobules that are nearly as large as the lateral lobes, as in P. faberi. All the proposed species obtained high support in phylogenetic analysis as new species. The recently described genus Apetalanthe is reduced to synonymy of Ponerorchis and a new combination is made.
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Affiliation(s)
- Dong-Liang Lin
- State Key Laboratory of Systematic and Evolutionary Botany and Herbarium, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, Yunnan, 650201, China
| | - André Schuiteman
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Chong-Bo Ma
- State Key Laboratory of Systematic and Evolutionary Botany and Herbarium, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Cheng Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, Yunnan, 650201, China
| | - Xue-Lian Guo
- State Key Laboratory of Systematic and Evolutionary Botany and Herbarium, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Shi-Si Chen
- State Key Laboratory of Systematic and Evolutionary Botany and Herbarium, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Xi-Long Wang
- Tibet Plateau Institute of Biology, Lhasa, Xizang 850001, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, Yunnan, 650201, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Mengla 666303, Yunnan, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany and Herbarium, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
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Wettewa E, Wallace LE. Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods. Mol Phylogenet Evol 2021; 157:107070. [PMID: 33421614 DOI: 10.1016/j.ympev.2021.107070] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/05/2020] [Accepted: 01/04/2021] [Indexed: 12/01/2022]
Abstract
Platanthera is one of the largest genera of temperate orchids in the Holarctic and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are North America and eastern Asia. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. While there is strong evidence that suggests monophyly of subgenus Limnorchis, most taxa in this group have not been included in a phylogenetic analysis. In this study, we developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, we collected high-throughput sequence data in 23 accessions of nine of the 12 diploid species of subgenus Limnorchis and outgroup species across Platanthera. A maximum likelihood analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3-4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Our results indicate complex biogeographic connections between Asia and North America, and therefore it suggests that Platanthera is a suitable system to test biogeographic hypotheses over time and space in the Holarctic. Our results are also expected to facilitate further study of diversification and biogeographic spread across Platanthera and lay the groundwork for understanding independent origins, biogeography, and morphological diversification of polyploid species within subgenus Limnorchis.
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Affiliation(s)
- Eranga Wettewa
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Lisa E Wallace
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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Lai YJ, Han Y, Schuiteman A, Chase MW, Xu SZ, Li JW, Wu JY, Yang BY, Jin XH. Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role. Mol Phylogenet Evol 2020; 157:107062. [PMID: 33387648 DOI: 10.1016/j.ympev.2020.107062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 11/28/2022]
Abstract
We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.
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Affiliation(s)
- Yang-Jun Lai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Yu Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Andre 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; Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Song-Zhi Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan 666303, China.
| | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), China
| | - Bo-Yun Yang
- School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China.
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Lahondère C, Vinauger C, Okubo RP, Wolff GH, Chan JK, Akbari OS, Riffell JA. The olfactory basis of orchid pollination by mosquitoes. Proc Natl Acad Sci U S A 2020; 117:708-16. [PMID: 31871198 DOI: 10.1073/pnas.1910589117] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nectar feeding by mosquitoes is important for survival and reproduction, and hence disease transmission. However, we know little about the sensory mechanisms that mediate mosquito attraction to sources of nectar, like those of flowers, or how this information is processed in the mosquito brain. Using a unique mutualism between Aedes mosquitoes and Platanthera obtusata orchids, we reveal that the orchid’s scent mediates this mutualism. Furthermore, lateral inhibition in the mosquito’s antennal (olfactory) lobe—via the neurotransmitter GABA—is critical for the representation of the scent. These results have implications for understanding the olfactory basis of mosquito nectar-seeking behaviors. Mosquitoes are important vectors of disease and require sources of carbohydrates for reproduction and survival. Unlike host-related behaviors of mosquitoes, comparatively less is understood about the mechanisms involved in nectar-feeding decisions, or how this sensory information is processed in the mosquito brain. Here we show that Aedes spp. mosquitoes, including Aedes aegypti, are effective pollinators of the Platanthera obtusata orchid, and demonstrate this mutualism is mediated by the orchid’s scent and the balance of excitation and inhibition in the mosquito’s antennal lobe (AL). The P. obtusata orchid emits an attractive, nonanal-rich scent, whereas related Platanthera species—not visited by mosquitoes—emit scents dominated by lilac aldehyde. Calcium imaging experiments in the mosquito AL revealed that nonanal and lilac aldehyde each respectively activate the LC2 and AM2 glomerulus, and remarkably, the AM2 glomerulus is also sensitive to N,N-diethyl-meta-toluamide (DEET), a mosquito repellent. Lateral inhibition between these 2 glomeruli reflects the level of attraction to the orchid scents. Whereas the enriched nonanal scent of P. obtusata activates the LC2 and suppresses AM2, the high level of lilac aldehyde in the other orchid scents inverts this pattern of glomerular activity, and behavioral attraction is lost. These results demonstrate the ecological importance of mosquitoes beyond operating as disease vectors and open the door toward understanding the neural basis of mosquito nectar-seeking behaviors.
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Chen SS, Guan BC. The complete chloroplast genome sequence of Platanthera minor. Mitochondrial DNA B Resour 2019; 5:63-64. [PMID: 33366423 PMCID: PMC7721053 DOI: 10.1080/23802359.2019.1696241] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/09/2019] [Indexed: 11/10/2022] Open
Abstract
Platanthera minor is widely distributed in East Asia. The complete circular chloroplast genome with a length of 154,430 bp possesses the typical structure, consisting of a large single copy (LSC) of 83,536 bp, a small single copy (SSC) of 17,612 bp, and two inverted repeats (IR) of 26,641 bp. The average GC content of the genome is 36.7%. The circular P. minor chloroplast genome contains 114 genes, including 80 protein-coding genes, four rRNA genes, and 30 tRNA genes. The chloroplast sequence provided a resource for analyzing genetic diversity of the Orchidaceae family.
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Affiliation(s)
- Si-Si Chen
- College of Life Sciences, Nanchang University, Nanchang, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bi-Cai Guan
- College of Life Sciences, Nanchang University, Nanchang, China
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Esposito F, Vereecken NJ, Gammella M, Rinaldi R, Laurent P, Tyteca D. Characterization of sympatric Platanthera bifolia and Platanthera chlorantha (Orchidaceae) populations with intermediate plants. PeerJ 2018; 6:e4256. [PMID: 29379684 PMCID: PMC5787349 DOI: 10.7717/peerj.4256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022] Open
Abstract
Platanthera bifolia and P. chlorantha are terrestrial and rewarding orchids with a wide Eurasian distribution. Although genetically closely related, they exhibit significant morphological, phenological and ecological differences that maintain reproductive isolation between the species. However, where both species co-occur, individuals with intermediate phenotypic traits, often considered as hybrids, are frequently observed. Here, we combined neutral genetic markers (AFLPs), morphometrics and floral scent analysis (GC-MS) to investigate two mixed Platanthera populations where morphologically intermediate plants were found. Self-pollination experiments revealed a low level of autogamy and artificial crossings combined with assessments of fruit set and seed viability, showed compatibility between the two species. The results of the genetic analyses showed that morphologically intermediate plants had similar genetic patterns as the P. bifolia group. These results are corroborated also by floral scent analyses, which confirmed a strong similarity in floral scent composition between intermediate morphotypes and P. bifolia. Therefore, this study provided a much more detailed picture of the genetic structure of a sympatric zone between two closely allied species and supports the hypothesis that intermediate morphotypes in sympatry could reflect an adaptive evolution in response to local pollinator-mediated selection.
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Affiliation(s)
- Fabiana Esposito
- Earth and Life Institute-Biodiversity Research Centre, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Rosita Rinaldi
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Pascal Laurent
- Unit of General Chemistry, Université Libre de Bruxelles, Brussels, Belgium
| | - Daniel Tyteca
- Earth and Life Institute-Biodiversity Research Centre, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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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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Gillespie LJ, Saarela JM, Sokoloff PC, Bull RD. New vascular plant records for the Canadian Arctic Archipelago. PhytoKeys 2015; 52:23-79. [PMID: 26311505 PMCID: PMC4549883 DOI: 10.3897/phytokeys.52.8721] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/15/2015] [Indexed: 06/04/2023]
Abstract
The Canadian Arctic Archipelago is a vast region of approximately 1,420,000 km(2), with a flora characterized by low species diversity, low endemicity, and little influence by alien species. New records of vascular plant species are documented here based on recent fieldwork on Victoria and Baffin Islands; additional records based on recent literature sources are mentioned. This paper serves as an update to the 2007 publication Flora of the Canadian Arctic Archipelago, and brings the total number of vascular plants for the region to 375 species and infraspecific taxa, an increase of 7.7%. Three families (Amaranthaceae, Juncaginaceae, Pteridaceae) and seven genera (Cherleria L., Cryptogramma R. Br., Platanthera Rich., Sabulina Rchb., Suaeda Forssk. ex J.F. Gmel., Triglochin L., Utricularia L.) are added to the flora, and one genus is deleted (Minuartia L.). Five species are first records for Nunavut (Arenarialongipedunculata Hultén, Cryptogrammastelleri (S.G. Gmel.) Prantl, Puccinelliabanksiensis Consaul, Saxifragaeschscholtzii Sternb., Utriculariaochroleuca R.W. Hartm.).
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Affiliation(s)
- Lynn J. Gillespie
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Jeffery M. Saarela
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Paul C. Sokoloff
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
| | - Roger D. Bull
- Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada
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Bateman RM, Rudall PJ, Bidartondo MI, Cozzolino S, Tranchida-Lombardo V, Carine MA, Moura M. Speciation via floral heterochrony and presumed mycorrhizal host switching of endemic butterfly orchids on the Azorean archipelago. Am J Bot 2014; 101:979-1001. [PMID: 24907253 DOI: 10.3732/ajb.1300430] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
• Premise of the study: Most orchid species native to the Macaronesian islands reflect immigration from western Europe or North Africa followed by anagenesis. The only putative exception is the butterfly orchids (Platanthera) of the Azores, where three species apparently reflect at least one cladogenetic speciation event. This multidisciplinary study explores the origin, speciation, phenotypic, and genotypic cohesion of these Azorean species and their mainland relatives.• Methods: Plants of Platanthera from 30 localities spanning all nine Azorean islands were compared with those of four continental European relatives for 38 morphometric characters; substantial subsets were also analyzed for plastid microsatellites, and for nrITS of both the orchids and their mycorrhizae.• Key results: Although the three Azorean and four mainland species are all readily distinguished morphometrically using several floral characters, and hybridization appears rare, divergence in ITS and especially plastid sequences is small. Despite occupying similar laurisilva habitats, the Azorean species differ radically in the identities and diversity of their mycorrhizal partners; specialism apparently increases rarity.• Conclusions: Although morphological evidence suggests two invasions of the islands from NW Africa and/or SW Europe, ITS data imply only one. As the molecular data are unable to distinguish among the potential mainland ancestors, two scenarios of relationship are explored that imply different ancestors. Both scenarios require both anagenetic and cladogenetic speciation events, involving homoplastic shifts in overall flower size and (often substantial) changes in the relative dimensions of individual floral organs. Limited genotypic divergence among the three species compared with greater phenotypic divergence suggests comparatively recent speciation. Mycorrhizae may be the most critical factor dictating the respective ecological tolerances, and thus the relative frequencies, of these species. The recent IUCN Red-List amalgamation of Azorean Platanthera taxa into a single species urgently requires reappraisal, as P. micrantha is an excellent indicator species of seminatural laurisilva forest and P. azorica is arguably Europe's rarest orchid.
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Affiliation(s)
| | - Paula J Rudall
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Martin I Bidartondo
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK Imperial College London, London, SW7 2AZ, UK
| | - Salvatore Cozzolino
- Department of Biology, University Federico II of Naples, Naples, I-80126, Italy
| | | | - Mark A Carine
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Mónica Moura
- CIBIO Research Center in Biodiversity and Genetic Resources-Azores, Department of Biology, University of the Azores, Rua Mae de Deus 58, Apartado 1422, 9501-801 Ponta Delgada, Portugal
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Bateman RM, Rudall PJ, Moura M. Systematic revision of Platanthera in the Azorean archipelago: not one but three species, including arguably Europe's rarest orchid. PeerJ 2013; 1:e218. [PMID: 24392284 PMCID: PMC3869205 DOI: 10.7717/peerj.218] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 11/20/2022] Open
Abstract
Background and Aims. The Macaronesian islands represent an excellent crucible for exploring speciation. This dominantly phenotypic study complements a separate genotypic study, together designed to identify and circumscribe Platanthera species (butterfly-orchids) on the Azores, and to determine their geographic origin(s) and underlying speciation mechanism(s). Methods. 216 individuals of Platanthera from 30 Azorean localities spanning all nine Azorean islands were measured for 38 morphological characters, supported by light and scanning electron microscopy of selected flowers. They are compared through detailed multivariate and univariate analyses with four widespread continental European relatives in the P. bifolia-chlorantha aggregate, represented by 154 plants from 25 populations, and with the highly misleading original taxonomic descriptions. Physiographic and ecological data were also recorded for each study population. Key Results. Despite limited genetic divergence, detailed phenotypic survey reveals not one or two but three discrete endemic species of Platanthera that are readily distinguished using several characters, most floral: P. pollostantha (newly named, formerly P. micrantha) occupies the widest range of habitats and altitudes and occurs on all nine islands; P. micrantha (formerly P. azorica) occurs on eight islands but is restricted to small, scattered populations in laurisilva scrub; the true P. azorica appears confined to a single volcanigenic ridge on the central island of São Jorge. Conclusions. Although hybridity seems low, the excess of phenotypic over genotypic divergence suggests comparatively recent speciation. The most probable of several credible scenarios is that Azorean Platantheras represent a single migration to the archipelago of airborne seed from ancestral population(s) located in southwest Europe rather than North America, originating from within the P. bifolia-chlorantha aggregate. We hypothesise that an initial anagenetic speciation event, aided by the founder effect, was followed by the independent origins of at least one of the two rarer endemic species from within the first-formed endemic species, via a cladogenetic speciation process that involved radical shifts in floral development, considerable phenotypic convergence, and increased mycorrhizal specificity. The recent amalgamation by IUCN of Azorean Platantheras into a single putative species on their Red List urgently requires overruling, as (a) P. azorica is arguably Europe's rarest bona fide orchid species and (b) the almost equally rare P. micrantha is one of the best indicators of semi-natural laurisilva habitats remaining on the Azores. Both species are threatened by habitat destruction and invasive alien plants. These orchids constitute a model system that illustrates the general advantages of circumscribing species by prioritising field-based over herbarium-based morphological approaches.
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Affiliation(s)
| | - Paula J Rudall
- Royal Botanic Gardens Kew, Richmond, Surrey , United Kingdom
| | - Mónica Moura
- CIBIO Research Center in Biodiversity and Genetic Resources - Azores, Department of Biology, University of the Azores , Ponta Delgada , Portugal
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Ross AA, Aldrich-Wolfe L, Lance S, Glenn T, Travers SE. Microsatellite markers in the western prairie fringed orchid, Platanthera praeclara (Orchidaceae). Appl Plant Sci 2013; 1:apps1200413. [PMID: 25202536 PMCID: PMC4105293 DOI: 10.3732/apps.1200413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 09/21/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Primers for 31 microsatellite-containing loci were developed for the threatened orchid Platanthera praeclara to enable characterization of the population genetics of this tallgrass prairie native. • METHODS AND RESULTS Sixteen polymorphic microsatellite loci were identified from four populations. Six of these loci were not in linkage disequilibrium. The average number of alleles per locus per population ranged from 6.4 to 8.9. • CONCLUSIONS The results indicate that six of the polymorphic loci will be useful in future studies of population structure, gene flow, and genetic diversity.
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Affiliation(s)
- Andrew A. Ross
- Department of Biological Sciences, NDSU Dept. 2715, North Dakota State University, Fargo, North Dakota 58108 USA
| | | | - Stacey Lance
- Environmental Health Science, University of Georgia, Athens, Georgia 30602 USA
| | - Travis Glenn
- Environmental Health Science, University of Georgia, Athens, Georgia 30602 USA
| | - Steven E. Travers
- Department of Biological Sciences, NDSU Dept. 2715, North Dakota State University, Fargo, North Dakota 58108 USA
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