151
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Li Y, Li Z, Hu Q, Zhai J, Liu Z, Wu S. Complete plastid genome of Apostasia shenzhenica (Orchidaceae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1591192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yunxia Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhanghai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qinglin Hu
- 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
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shasha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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Valoroso MC, Sobral R, Saccone G, Salvemini M, Costa MMR, Aceto S. Evolutionary Conservation of the Orchid MYB Transcription Factors DIV, RAD, and DRIF. FRONTIERS IN PLANT SCIENCE 2019; 10:1359. [PMID: 31736999 PMCID: PMC6838138 DOI: 10.3389/fpls.2019.01359] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 05/02/2023]
Abstract
The MYB transcription factors DIVARICATA (DIV), DIV-and-RAD-Interacting-Factor (DRIF), and the small interfering peptide RADIALIS (RAD) can interact, forming a regulatory module that controls different plant developmental processes. In the snapdragon Antirrhinum majus, this module, together with the TCP transcription factor CYCLOIDEA (CYC), is responsible for the establishment of floral dorsoventral asymmetry. The spatial gene expression pattern of the OitDIV, OitDRIF, and OitRAD homologs of Orchis italica, an orchid with zygomorphic flowers, has suggested a possible conserved role of these genes in bilateral symmetry of the orchid flower. Here, we have identified four DRIF genes of orchids and have reconstructed their genomic organization and evolution. In addition, we found snapdragon transcriptional cis-regulatory elements of DIV and RAD loci generally conserved within the corresponding orchid orthologues. We have tested the biochemical interactions among OitDIV, OitDRIF1, and OitRAD of O. italica, showing that OitDRIF1 can interact both with OitDIV and OitRAD, whereas OitDIV and OitRAD do not directly interact, as in A. majus. The analysis of the quantitative expression profile of these MYB genes revealed that in zygomorphic orchid flowers, the DIV, DRIF1, and RAD transcripts are present at higher levels in the lip than in lateral inner tepals, whereas in peloric orchid flowers they show similar expression levels. These results indicate that MYB transcription factors could have a role in shaping zygomorphy of the orchid flower, potentially enriching the underlying orchid developmental code.
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Affiliation(s)
| | - Rómulo Sobral
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Giuseppe Saccone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Manuela Ribeiro Costa
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, Naples, Italy
- *Correspondence: Serena Aceto,
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153
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Kuo YT, Chao YT, Chen WC, Shih MC, Chang SB. Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. ANNALS OF BOTANY 2019; 123:69-77. [PMID: 30113635 PMCID: PMC6344096 DOI: 10.1093/aob/mcy136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/22/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Orchidaceae is a large plant family, and its extraordinary adaptations may have guaranteed its evolutionary success. Flavonoids are a group of secondary metabolites that mediate plant acclimation to challenge environments. Chalcone synthase (CHS) catalyses the initial step in the flavonoid biosynthetic pathway. This is the first chromosome-level investigation of the CHS gene family in Phalaenopsis aphrodite and was conducted to elucidate if divergence of this gene family is associated with chromosome evolution. METHODS Complete CHS genes were identified from our whole-genome sequencing data sets and their gene expression profiles were obtained from our transcriptomic data sets. Fluorescence in situ hybridization (FISH) was conducted to position five CHS genes to high-resolution pachytene chromosomes. KEY RESULTS The five Phalaenopsis CHS genes can be classified into three groups, PaCHS1, PaCHS2 and the tandemly arrayed three-gene cluster, which diverged earlier than those of the orchid genera and species. Additionally, pachytene chromosome-based FISH mapping showed that the three groups of CHS genes are localized on three distinct chromosomes. Moreover, an expression analysis of RNA sequencing revealed that the five CHS genes had highly differentiated expression patterns and its expression pattern-based clustering showed high correlations between sequence divergences and chromosomal localizations of the CHS gene family in P. aphrodite. CONCLUSIONS Based on their phylogenetic relationships, expression clustering analysis and chromosomal distributions of the five paralogous PaCHS genes, we proposed that expansion of this gene family in P. aphrodite occurred through segmental duplications, followed by tandem duplications. These findings provide information for further studies of CHS functions and regulations, and shed light on the divergence of an important gene family in orchids.
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Affiliation(s)
- Yi-Tzu Kuo
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- For correspondence. E-mail:
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154
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Strullu-Derrien C, Selosse MA, Kenrick P, Martin FM. The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. THE NEW PHYTOLOGIST 2018; 220:1012-1030. [PMID: 29573278 DOI: 10.1111/nph.15076] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/14/2018] [Indexed: 05/05/2023]
Abstract
Contents Summary 1012 I. Introduction 1013 II. The mycorrhizal symbiosis at the dawn and rise of the land flora 1014 III. From early land plants to early trees: the origin of roots and true mycorrhizas 1016 IV. The diversification of the AM symbiosis 1019 V. The ECM symbiosis 1021 VI. The recently evolved ericoid and orchid mycorrhizas 1023 VII. Limits of paleontological vs genetic approaches and perspectives 1023 Acknowledgements 1025 References 1025 SUMMARY: The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.
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Affiliation(s)
- Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Francis M Martin
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
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Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Mol Phylogenet Evol 2018; 129:27-47. [DOI: 10.1016/j.ympev.2018.07.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/25/2018] [Accepted: 07/15/2018] [Indexed: 11/20/2022]
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156
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Lamont BB, He T, Yan Z. Evolutionary history of fire‐stimulated resprouting, flowering, seed release and germination. Biol Rev Camb Philos Soc 2018; 94:903-928. [DOI: 10.1111/brv.12483] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Byron B. Lamont
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Tianhua He
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China
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158
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Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. Proc Natl Acad Sci U S A 2018; 115:12471-12476. [PMID: 30397141 DOI: 10.1073/pnas.1809326115] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species richness is greatest in the tropics, and much of this diversity is concentrated in mountains. Janzen proposed that reduced seasonal temperature variation selects for narrower thermal tolerances and limited dispersal along tropical elevation gradients [Janzen DH (1967) Am Nat 101:233-249]. These locally adapted traits should, in turn, promote reproductive isolation and higher speciation rates in tropical mountains compared with temperate ones. Here, we show that tropical and temperate montane stream insects have diverged in thermal tolerance and dispersal capacity, two key traits that are drivers of isolation in montane populations. Tropical species in each of three insect clades have markedly narrower thermal tolerances and lower dispersal than temperate species, resulting in significantly greater population divergence, higher cryptic diversity, higher tropical speciation rates, and greater accumulation of species over time. Our study also indicates that tropical montane species, with narrower thermal tolerance and reduced dispersal ability, will be especially vulnerable to rapid climate change.
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159
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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160
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Gaskett AC, Gallagher RV. Orchid diversity: Spatial and climatic patterns from herbarium records. Ecol Evol 2018; 8:11235-11245. [PMID: 30519440 PMCID: PMC6262934 DOI: 10.1002/ece3.4598] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/10/2018] [Accepted: 09/16/2018] [Indexed: 01/31/2023] Open
Abstract
AIM We test for spatial and climatic patterns of diversification in the Orchidaceae, an angiosperm family characterized by high levels of species diversity and rarity. Globally, does orchid diversity correlate with land area? In Australia, does diversity correlate with herbarium collecting effort, range size, or climate niche breadth? Where are Australia's orchids distributed spatially, in protected areas, and in climate space? LOCATION Global, then Australia. METHODS We compared orchid diversity with land area for continents and recognized orchid diversity hotspots. Then, we used cleaned herbarium records to compare collecting effort (for Australian Orchidaceae vs. all other plant families, and also among orchid genera). Spatial and climate distributions were mapped to determine orchids' coverage in the protected area network, range sizes, and niche breadths. RESULTS Globally, orchid diversity does not correlate with land area (depauperate regions are the subantarctic: 10 species, and northern North America: 394 species). Australian herbarium records and collecting effort generally reflect orchid species diversity (1,583 spp.), range sizes, and niche breadths. Orchids are restricted to 13% of Australia's landmass with 211 species absent from any protected areas. Species richness is the greatest in three biomes with high general biodiversity: Temperate (especially southwest and southeast Australia), Tropical, and Subtropical (coastal northern Queensland). Absence from the Desert is consistent with our realized climate niche-orchids avoid high temperature/low rainfall environments. Orchids have narrower range sizes than nonorchid species. Highly diverse orchid genera have narrower rainfall breadths than less diverse genera. MAIN CONCLUSIONS Herbarium data are adequate for testing hypotheses about Australian orchids. Distribution is likely driven by environmental factors. In contrast, diversification did not correlate with increases in range size, rainfall, or temperature breadths, suggesting speciation does not occur via invasion and local adaptation to new habitats. Instead, diversification may rely on access to extensive obligate symbioses with mycorrhizae and/or pollinators.
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Affiliation(s)
- Anne C. Gaskett
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Rachael V. Gallagher
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
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161
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Texier N, Deblauwe V, Stévart T, Sonké B, Simo-Droissart M, Azandi L, Bose R, Djuikouo MN, Kamdem G, Kamdem N, Mayogo S, Zemagho L, Droissart V. Spatio-temporal patterns of orchids flowering in Cameroonian rainforests. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2018; 62:1931-1944. [PMID: 30215186 DOI: 10.1007/s00484-018-1594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
We characterized the flowering patterns of 45 epiphytic orchid species occurring in Cameroonian rainforests to explore the environmental and evolutionary forces driving their phenology. We used a dataset of 3470 flowering events recorded over a period of 11 years in the Yaoundé living collection (82% of the flowering events) and from in situ observations (18% of the flowering events) to (i) describe flowering frequency and timing and synchronization among taxa; (ii) test flowering patterns for phylogenetic relatedness at the generic level; and (iii) investigate the spatial patterns of phenology. An annual flowering pattern prevailed among the species selected for this study. The species-rich African genera Angraecum and Polystachya are characterized by subannual and annual frequency patterns, respectively. However, in terms of flowering time, no phylogenetic signal was detected for the four most diverse genera (Ancistrorhynchus, Angraecum, Bulbophyllum, and Polystachya). Results suggest also an important role of photoperiod and precipitation as climatic triggers of flowering patterns. Moreover, 16% of the taxa cultivated ex situ, mostly Polystachya, showed significant differences in flowering time between individuals originating from distinct climatic regions, pointing toward the existence of phenological ecotypes. Phenological plasticity, suggested by the lack of synchronized flowering in spatially disjunct populations of Polystachya, could explain the widespread radiation of this genus throughout tropical Africa. Our study highlights the need to take the spatial pattern of flowering time into account when interpreting phylogeographic patterns in central African rainforests.
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Affiliation(s)
- N Texier
- Faculty of Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, CP160/12, 50 Av. F. Roosevelt, 1050, Brussels, Belgium.
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium.
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon.
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA.
| | - V Deblauwe
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture, Yaoundé, Cameroon
| | - T Stévart
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
- Agentschap Plantentuin Meise, Domein van Bouchout, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - B Sonké
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
| | - M Simo-Droissart
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - L Azandi
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - R Bose
- AMAP, IRD, CIRAD, CNRS, INRA, Univ Montpellier, Montpellier, France
| | - M-N Djuikouo
- Department of Botany and Plant Physiology, University of Buea, Buea, Cameroon
| | - G Kamdem
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - N Kamdem
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - S Mayogo
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - L Zemagho
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - V Droissart
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
- AMAP, IRD, CIRAD, CNRS, INRA, Univ Montpellier, Montpellier, France
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D'Agostino N, Tamburino R, Cantarella C, De Carluccio V, Sannino L, Cozzolino S, Cardi T, Scotti N. The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution. Genes (Basel) 2018; 9:E503. [PMID: 30336638 PMCID: PMC6210379 DOI: 10.3390/genes9100503] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022] Open
Abstract
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.
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Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Valentina De Carluccio
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
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Miura C, Yamaguchi K, Miyahara R, Yamamoto T, Fuji M, Yagame T, Imaizumi-Anraku H, Yamato M, Shigenobu S, Kaminaka H. The Mycoheterotrophic Symbiosis Between Orchids and Mycorrhizal Fungi Possesses Major Components Shared with Mutualistic Plant-Mycorrhizal Symbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1032-1047. [PMID: 29649962 DOI: 10.1094/mpmi-01-18-0029-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Achlorophylous and early developmental stages of chorolophylous orchids are highly dependent on carbon and other nutrients provided by mycorrhizal fungi, in a nutritional mode termed mycoheterotrophy. Previous findings have implied that some common properties at least partially underlie the mycorrhizal symbioses of mycoheterotrophic orchids and that of autotrophic arbuscular mycorrhizal (AM) plants; however, information about the molecular mechanisms of the relationship between orchids and their mycorrhizal fungi is limited. In this study, we characterized the molecular basis of an orchid-mycorrhizal (OM) symbiosis by analyzing the transcriptome of Bletilla striata at an early developmental stage associated with the mycorrhizal fungus Tulasnella sp. The essential components required for the establishment of mutual symbioses with AM fungi or rhizobia in most terrestrial plants were identified from the B. striata gene set. A cross-species gene complementation analysis showed one of the component genes, calcium and calmodulin-dependent protein kinase gene CCaMK in B. striata, retains functional characteristics of that in AM plants. The expression analysis revealed the activation of homologs of AM-related genes during the OM symbiosis. Our results suggest that orchids possess, at least partly, the molecular mechanisms common to AM plants.
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Affiliation(s)
- Chihiro Miura
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- 2 Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Ryohei Miyahara
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tatsuki Yamamoto
- 3 Graduate School of Agriculture, Tottori University, Tottori, Japan
| | - Masako Fuji
- 1 Faculty of Agriculture, Tottori University, Tottori, Japan
| | | | - Haruko Imaizumi-Anraku
- 5 Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan; and
| | | | - Shuji Shigenobu
- 2 Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
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164
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Australasian orchid biogeography at continental scale: Molecular phylogenetic insights from the Sun Orchids (Thelymitra, Orchidaceae). Mol Phylogenet Evol 2018; 127:304-319. [DOI: 10.1016/j.ympev.2018.05.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/07/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
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165
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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] [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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166
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Cardoso-Gustavson P, Saka MN, Pessoa EM, Palma-Silva C, Pinheiro F. Unidirectional transitions in nectar gain and loss suggest food deception is a stable evolutionary strategy in Epidendrum (Orchidaceae): insights from anatomical and molecular evidence. BMC PLANT BIOLOGY 2018; 18:179. [PMID: 30180799 PMCID: PMC6122447 DOI: 10.1186/s12870-018-1398-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Nectar gain and loss are important flower transitions observed in angiosperms, and are particularly common in orchids. To understand such transitions, the availability of detailed anatomical data and species-level phylogenies are crucial. We investigated the evolution of food deception in Epidendrum, one of the largest orchid genera, using genus phylogeny to map transitions between nectar gain and loss among different clades. Associations between anatomical and histochemical changes and nectar gain and loss were examined using fresh material available from 27 species. The evolution of nectar presence/absence in Epidendrum species was investigated in a phylogenetic framework of 47 species, using one nuclear and five plastid DNA regions available from GenBank and sequenced in this study. RESULTS The presence or absence of nectar was strongly associated with changes in the inner epidermal tissues of nectaries. Nectar-secreting species have unornamented epidermal tissue, in contrast to the unicellular trichomes found on the epidermis of food deceptive species. Bayesian tests confirmed that transitions occurred preferentially from nectar presence to nectar absence across the Epidendrum phylogeny. In addition, independent nectar loss events were found across the phylogeny, suggesting a lack of constraint for these transitions. CONCLUSIONS Ornamented nectaries may play an important role in the deceptive pollination strategy by secreting volatile organic compounds and providing tactile stimuli to pollinators. The recurrent and apparently irreversible pattern of nectar loss in Epidendrum suggests that food deception may constitute an alternative evolutionarily stable strategy, as observed in other orchid groups.
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Affiliation(s)
| | - Mariana Naomi Saka
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP 13506-900 Brazil
| | - Edlley Max Pessoa
- Centro de Ciências Biológicas, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE 50670-420 Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862 Brazil
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862 Brazil
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167
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Tallowin OJ, Tamar K, Meiri S, Allison A, Kraus F, Richards SJ, Oliver PM. Early insularity and subsequent mountain uplift were complementary drivers of diversification in a Melanesian lizard radiation (Gekkonidae: Cyrtodactylus). Mol Phylogenet Evol 2018; 125:29-39. [DOI: 10.1016/j.ympev.2018.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 02/20/2018] [Accepted: 03/14/2018] [Indexed: 11/30/2022]
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168
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Zhang S, Yang Y, Li J, Qin J, Zhang W, Huang W, Hu H. Physiological diversity of orchids. PLANT DIVERSITY 2018; 40:196-208. [PMID: 30740565 PMCID: PMC6137271 DOI: 10.1016/j.pld.2018.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/09/2018] [Accepted: 06/20/2018] [Indexed: 05/04/2023]
Abstract
The Orchidaceae is a diverse and wide spread family of flowering plants that are of great value in ornamental, medical, conservation, and evolutionary research. The broad diversity in morphology, growth form, life history, and habitat mean that the members of Orchidaceae exhibit various physiological properties. Epiphytic orchids are often characterized by succulent leaves with thick cell walls, cuticles, and sunken stomata, whereas terrestrial orchids possess rhizomes, corms, or tubers. Most orchids have a long juvenile period, slow growth rate, and low photosynthetic capacity. This reduced photosynthetic potential can be largely explained by CO2 diffusional conductance and leaf internal structure. The amount of light required for plant survival depends upon nutritional mode, growth form, and habitat. Most orchids can adapt to their light environments through morphological and physiological adjustments but are sensitive to sudden changes in irradiance. Orchids that originate from warm regions are susceptible to chilling temperatures, whereas alpine members are vulnerable to high temperatures. For epiphytic orchids, rapid water uptake by the velamen radicum, water storage in their pseudobulbs and leaves, slow water loss, and Crassulacean Acid Metabolism contribute to plant-water balance and tolerance to drought stress. The presence of the velamen radicum and mycorrhizal fungi may compensate for the lack of root hairs, helping with quick absorbance of nutrients from the atmosphere. Under cultivation conditions, the form and concentration of nitrogen affect orchid growth and flowering. However, the limitations of nitrogen and phosphorous on epiphytic orchids in the wild, which require these plants to depend on mycorrhizal fungi for nutrients throughout the entire life cycle, are not clearly understood. Because they lack endosperm, seed germination depends upon obtaining nutrients via mycorrhizal fungi. Adult plants of some autotrophic orchids also gain carbon, nitrogen, phosphorus, and other elements from their mycorrhizal partners. Future studies should examine the mechanisms that determine slow growth and flower induction, the physiological causes of variations in flowering behavior and floral lifespan, the effects of nutrients and atmospheric-nitrogen deposition, and practical applications of mycorrhizal fungi in orchid cultivation.
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Affiliation(s)
- Shibao Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yingjie Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Li
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Qin
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei Huang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong Hu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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169
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Cahenzli F, Bonetti C, Erhardt A. Divergent strategies in pre- and postzygotic reproductive isolation between two closely related Dianthus species. Evolution 2018; 72:1851-1862. [PMID: 30003537 DOI: 10.1111/evo.13556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
Abstract
Quantifying the relative contribution of multiple isolation barriers to gene flow between recently diverged species is essential for understanding speciation processes. In parapatric populations, local adaptation is thought to be a major contributor to the evolution of reproductive isolation. However, extrinsic postzygotic barriers assessed in reciprocal transplant experiments are often neglected in empirical assessments of multiple isolation barriers. We analyzed multiple isolation barriers between two closely related species of the plant genus Dianthus, a genus characterized by the most rapid species diversification in plants reported so far. Although D. carthusianorum L. and D. sylvestris Wulf. can easily be hybridized in crossing experiments, natural hybrids are rare. We found that in parapatry, pollinator-mediated prezygotic reproductive isolation barriers are important for both D. carthusianorum (0.761) and D. sylvestris (0.468). In contrast to D. carthusianorum, high hybrid viability in D. sylvestris (-0.491) was counteracted by strong extrinsic postzygotic isolation (0.900). Our study highlights the importance of including reciprocal transplant experiments for documenting extrinsic postzygotic isolation and demonstrates clearly divergent strategies and hence asymmetric pre- and postzygotic reproductive isolation between closely related species. It also suggests that pollinator-mediated and ecological isolation could have interacted in synergistic ways, further stimulating rapid speciation in Dianthus.
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Affiliation(s)
- Fabian Cahenzli
- Forschungsinstitut für biologischen Landbau (FiBL), Department of crop Sciences, Ackerstrasse 113, CH-5070, Frick, Switzerland
| | - Christophe Bonetti
- Department of Environmental Sciences, Section Conservation Biology (NLU), University of Basel, St. Johanns-Vorstadt 10, CH-4056, Basel, Switzerland
| | - Andreas Erhardt
- Department of Environmental Sciences, Botany, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
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170
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Canal D, Köster N, Jones KE, Korotkova N, Croat TB, Borsch T. Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes. AMERICAN JOURNAL OF BOTANY 2018; 105:1035-1052. [PMID: 29995336 DOI: 10.1002/ajb2.1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence-time estimates and diversification rate shift analyses. METHODS We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures. KEY RESULTS We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well-supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya. CONCLUSIONS Philodendron is a species-rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined.
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Affiliation(s)
- Dubán Canal
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Nils Köster
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Katy E Jones
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Nadja Korotkova
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Thomas B Croat
- Missouri Botanical Garden, Monsanto Research Building, P.O. Box 299, St. Louis, Missouri, 63166, USA
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
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171
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Tao Z, Ren Z, Bernhardt P, Liang H, Li H, Zhao Y, Wang H, Li D. Does reproductive isolation reflect the segregation of color forms in Spiranthes sinensis (Pers.) Ames complex (Orchidaceae) in the Chinese Himalayas? Ecol Evol 2018; 8:5455-5469. [PMID: 29938065 PMCID: PMC6010815 DOI: 10.1002/ece3.4067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 01/16/2023] Open
Abstract
Isolation between species, or taxa sharing a common lineage, depends primarily on the relative strengths of various reproductive barriers. Previous studies on reproductive isolation between orchids emphasized mechanical and ethological barriers in flowers of species showing food and/or sexual mimicry. In this study, we investigated and quantified a series of prepollination and postpollination barriers between pink and white forms of Spiranthes sinensis sl, a nectar-secreting complex. We generated ML trees based on trnS-G and matK to explore phylogenetic relationships in this species complex. Spiranthes sinensis sl segregated from some other congeners, but the white form constituted a distinct clade in relation to the pink form. The white form secreted 2-Phenylethanol as it is a single-scent compound and was pollinated almost exclusively by native, large-bodied Apis cerana and Bombus species (Apidae). Apis cerana showed a high floral constancy to this form. The scentless, pink form was pollinated primarily by smaller bees in the genera Ceratina (Apidae), and members of the family Halictidae, with infrequent visits by A. cerana and Bombus species. Fruit set and the production of large embryos following interform pollination treatments were significantly lower compared to intraform pollination results for the white form. Our results suggested that pollinator isolation, based on color and scent cues, may result in greater floral constancy in white populations when both forms are sympatric as two different, guilds of pollinators forage selectively preventing or reducing prospective gene flow. Postpollination barriers appear weaker than prepollination barriers but they also play a role in interform isolation, especially in the white form. Our findings suggest that floral color forms in S. sinensis do not represent an unbalanced polymorphism. Interpretations of the evolutionary status of these forms are discussed.
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Affiliation(s)
- Zhi‐Bin Tao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Zong‐Xin Ren
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | | | - Huan Liang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Hai‐Dong Li
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Yan‐Hui Zhao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
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172
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Zhang H, Jin J, Moore MJ, Yi T, Li D. Plastome characteristics of Cannabaceae. PLANT DIVERSITY 2018; 40:127-137. [PMID: 30175293 PMCID: PMC6114266 DOI: 10.1016/j.pld.2018.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/11/2018] [Accepted: 04/18/2018] [Indexed: 05/02/2023]
Abstract
Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species. To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330-983 bp) into the Large Single-Copy (LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell (BS = 100). Celtis, Cannabis-Humulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support (BS = 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.
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Affiliation(s)
- Huanlei Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming 650201, China
| | - Jianjun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming 650201, China
| | | | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Corresponding author.
| | - Dezhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Corresponding author.
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173
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Fog Water Is Important in Maintaining the Water Budgets of Vascular Epiphytes in an Asian Tropical Karst Forests during the Dry Season. FORESTS 2018. [DOI: 10.3390/f9050260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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174
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Barrett CF, Wicke S, Sass C. Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex. THE NEW PHYTOLOGIST 2018; 218:1192-1204. [PMID: 29502351 PMCID: PMC5902423 DOI: 10.1111/nph.15072] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 05/08/2023]
Abstract
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here, we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of genomic change among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help to fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 5218 Life Sciences Building, 53 Campus Drive, Morgantown, WV 26501, USA
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, 48149 Muenster, Germany
| | - Chodon Sass
- Department of Plant and Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, California 94720, USA
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175
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Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Mol Phylogenet Evol 2018; 122:59-79. [DOI: 10.1016/j.ympev.2018.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
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176
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Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC. Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:631-640. [PMID: 29608785 DOI: 10.1002/ajb2.1047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
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Affiliation(s)
- Sarah A Unruh
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung 404, Taiwan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Science Museum, Amakubo, Tsukuba, 305-0005, Japan
| | | | - Richard P Shefferson
- Organization for Programs on Environmental Sciences, University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Ann Smithson
- Smithson Environmental Consultancy & DNALabs Environmental Genetics Testing, Bassendean, Western Australia, 6054
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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177
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Valencia-Nieto B, Sosa V, Márquez-Guzmán J. Anther development in tribe Epidendreae: orchids with contrasting pollination syndromes. PeerJ 2018; 6:e4383. [PMID: 29503766 PMCID: PMC5833465 DOI: 10.7717/peerj.4383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/29/2018] [Indexed: 12/01/2022] Open
Abstract
Background Epidendreae is one of the most diverse tribes among the orchids with remarkable variation in life form, floral morphology and pollination syndromes. Its circumscription was recently revised and subtribes Agrostophyllinae and Calypsoinae were transferred into this tribe. One of the principal floral characters utilized in classification of orchids is the incumbency or bending of the column. This study records and compares late stages of anther, column and lip development, and discusses anther characters in fifteen representative taxa of five of the six subtribes in Epidendreae with respect to classification and pollination biology. Methods A series of late floral stages were sampled and fixed for examination under scanning electron microscope. Results Anther incumbency or bending in this group varies from 90° to almost 180°. Incumbency in the late stages of development is reached in Bletiinae, Ponerinae, Pleurothallidinae and Laeliinae whereas incumbency is reached early in its development in Corallorhiza and Govenia of Calypsoinae. Discussion Our observations indicate that the position of Chysis in subtribe Bletiinae needs revision based on differences in a number floral, and in particular of anther characters; and that Coelia only shares the early anther incumbency with Calypsoinae members, but not the rest of floral and anther characters. Anatomical characters such as crystals around the actinocytic stomata on the anther cap and sugar crystals in Laeliinae; lack of rostellum in Bletiinae; coalescent anther with the column, lack of trichomes and papillae on lip keels, and underdeveloped rostellum in Chysis; a mechanism by which the anther cap comes off (it is joined with the grooved lip by a claw) in Isochilus are all related to pollination syndromes and reproductive biology.
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Affiliation(s)
- Benjamín Valencia-Nieto
- Laboratorio de Desarrollo en Plantas, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, CDMX, México
| | - Victoria Sosa
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, México
| | - Judith Márquez-Guzmán
- Laboratorio de Desarrollo en Plantas, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, CDMX, México
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178
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Surveswaran S, Gowda V, Sun M. Using an integrated approach to identify cryptic species, divergence patterns and hybrid species in Asian ladies' tresses orchids (Spiranthes, Orchidaceae). Mol Phylogenet Evol 2018; 124:106-121. [PMID: 29501785 DOI: 10.1016/j.ympev.2018.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/08/2023]
Abstract
Spiranthes (∼36 species, Orchidaceae) is a small genus with a global distribution. It has a center of diversity in North America with only a few species occurring in Asia. This study focuses on the Asian Spiranthes with an emphasis on understanding their biogeographic relationships and species delimitations using molecular markers. Our phylogenetic trees based on nuclear (ITS) and chloroplast (trnL-trnLF, matK and trnS-G) sequences from samples across their range in Asia revealed the Asian Spiranthes are monophyletic. Ancestral area optimization suggested that North America forms the ancestral region for the Asian Spiranthes rather than Europe suggesting that they originated from a single long-distance dispersal event. Our study also revealed the presence of a cryptic species S. himalayensis, which was discovered based on molecular data thus emphasizing the importance of wide geographical sampling in phylogenetic studies. Sequences of cloned ITS provided support for the hypothesis that natural hybridization between S. sinensis and the newly described S. himalayensis resulted in the allotetraploid S. hongkongensis, with S. himalayensis as the paternal parent. One of the species complexes known in Asia is the S. sinensis complex, which shows a wide occurrence and is known for local geographical variants. Some of these variants have been described as new species in Australia and New Zealand. Our studies show that all the sampled variants including the Australian and New Zealand species show monophyly despite having long branches. This suggests that there may be high rates of gene flow between the geographically distinct forms resulting in lack of species resolution within the S. sinensis complex.
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Affiliation(s)
- Siddharthan Surveswaran
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.
| | - Mei Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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179
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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: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [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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181
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Smith SA, Brown JW. Constructing a broadly inclusive seed plant phylogeny. AMERICAN JOURNAL OF BOTANY 2018; 105:302-314. [PMID: 29746720 DOI: 10.1002/ajb2.1019] [Citation(s) in RCA: 368] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/19/2017] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade. KEY RESULTS The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants. CONCLUSIONS This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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182
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Condamine FL, Rolland J, Höhna S, Sperling FAH, Sanmartín I. Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies. Syst Biol 2018; 67:940-964. [DOI: 10.1093/sysbio/syy009] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l’Evolution (Université de Montpellier
- CNRS IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Jonathan Rolland
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilian-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried 82152, Germany
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
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183
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Wang YH, Wicke S, Wang H, Jin JJ, Chen SY, Zhang SD, Li DZ, Yi TS. Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:138. [PMID: 29479365 PMCID: PMC5812350 DOI: 10.3389/fpls.2018.00138] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/24/2018] [Indexed: 05/18/2023]
Abstract
The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes. The plastomes of Cercidoideae all exhibited a typical quadripartite structure with a conserved gene content typical of most angiosperm plastomes. Plastome size ranged from 151,705 to 165,416 bp, mainly due to the expansion and contraction of inverted repeat (IR) regions. The order of genes varied due to the occurrence of several inversions. In Tylosema species, a plastome with a 29-bp IR-mediated inversion was found to coexist with a canonical-type plastome, and the abundance of the two arrangements of isomeric molecules differed between individuals. Complete plastome data were much more efficient at resolving intergeneric relationships of Cercidoideae than the previously used selection of only a few plastid or nuclear loci. In sum, our study revealed novel insights into the structural diversification of plastomes in an early-branching legume lineage, and, thus, into the evolutionary trajectories of legume plastomes in general.
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Affiliation(s)
- Yin-Huan Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Ting-Shuang Yi
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
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184
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Novotná A, Benítez Á, Herrera P, Cruz D, Filipczyková E, Suárez JP. High diversity of root-associated fungi isolated from three epiphytic orchids in southern Ecuador. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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185
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
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186
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Niu Z, Xue Q, Wang H, Xie X, Zhu S, Liu W, Ding X. Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus. Int J Mol Sci 2017; 18:E2307. [PMID: 29099062 PMCID: PMC5713276 DOI: 10.3390/ijms18112307] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/27/2017] [Accepted: 10/20/2017] [Indexed: 01/03/2023] Open
Abstract
The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces-selection, mutational biases, and GC-biased gene conversion (gBGC)-on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus.
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Affiliation(s)
- Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Hui Wang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Xuezhu Xie
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Shuying Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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187
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Pérez-Escobar OA, Chomicki G, Condamine FL, de Vos JM, Martins AC, Smidt EC, Klitgård B, Gerlach G, Heinrichs J. Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin's Favourite Orchids. Sci Rep 2017; 7:12878. [PMID: 29018291 PMCID: PMC5635016 DOI: 10.1038/s41598-017-12300-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/06/2017] [Indexed: 11/17/2022] Open
Abstract
Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.
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Affiliation(s)
| | - Guillaume Chomicki
- Department of Plant Sciences, University of Oxford, South Park Road, OX1 3RB, Oxford, United Kingdom
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut de Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Jurriaan M de Vos
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, TW9 3AB, United Kingdom.
- Department of Environmental Sciences - Botany, University of Basel, Totengässlein 3, 4051, Basel, Switzerland.
| | - Aline C Martins
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Eric C Smidt
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Bente Klitgård
- Department of Identification and Naming, Royal Botanic Gardens Kew, Richmond, TW9 3AB, UK
| | - Günter Gerlach
- Botanischer Garten München, Menzinger Straße 67, D-80638, München, Germany
| | - Jochen Heinrichs
- Department für Biologie I, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universität, Menzinger Straße 67, D-80638, München, Germany
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188
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Niu Z, Pan J, Zhu S, Li L, Xue Q, Liu W, Ding X. Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids. FRONTIERS IN PLANT SCIENCE 2017; 8:1713. [PMID: 29046685 PMCID: PMC5632729 DOI: 10.3389/fpls.2017.01713] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/20/2017] [Indexed: 05/23/2023]
Abstract
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci-ndhA intron, matK-5'trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3'trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32-that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.
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Affiliation(s)
- Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiajia Pan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuying Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ludan Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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189
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. The Apostasia genome and the evolution of orchids. Nature 2017; 549:379-383. [PMID: 28902843 PMCID: PMC7416622 DOI: 10.1038/nature23897] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica4, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
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Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
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190
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Mutualisms Are Not on the Verge of Breakdown. Trends Ecol Evol 2017; 32:727-734. [PMID: 28739078 DOI: 10.1016/j.tree.2017.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 11/21/2022]
Abstract
Mutualisms teeter on a knife-edge between conflict and cooperation, or so the conventional wisdom goes. The costs and benefits of mutualism often depend on the abiotic or biotic context in which an interaction occurs, and experimental manipulations can induce shifts in interaction outcomes from mutualism all the way to parasitism. Yet, research suggests that mutualisms rarely turn parasitic in nature. Similarly, despite the potential for 'cheating' to undermine mutualism evolution, empirical evidence for fitness conflicts between partners and, thus, selection for cheating in mutualisms is scant. Furthermore, mutualism seldom leads to parasitism at macroevolutionary timescales. Thus, I argue here that mutualisms do not deserve their reputation for ecological and evolutionary instability, and are not on the verge of breakdown.
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191
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Krawczyk K, Wiland-Szymańska J, Buczkowska-Chmielewska K, Drapikowska M, Maślak M, Myszczyński K, Szczecińska M, Ślipiko M, Sawicki J. The complete chloroplast genome of a rare orchid species Liparis loeselii (L.). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0809-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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192
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Levy Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I. TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Res 2017; 45:W260-W264. [PMID: 28453644 PMCID: PMC5570260 DOI: 10.1093/nar/gkx288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Accepted: 04/26/2017] [Indexed: 11/23/2022] Open
Abstract
Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype. To this end, it considers alternative histories of whole-organism phenotypic changes, which result in the extant phenotypic states. Its joint likelihood framework that combines models of sequence and phenotype evolution allows testing whether an association between these processes exists. In addition to predicting sequence sites most likely to be associated with the phenotypic trait, the server can optionally integrate structural 3D information. This integration allows a visual detection of trait-associated sequence sites that are juxtapose in 3D space, thereby suggesting a common functional role. We used TraitRateProp to study the shifts in sequence evolution rate of the RPS8 protein upon transitions into heterotrophy in Orchidaceae. TraitRateProp is available at http://traitrate.tau.ac.il/prop.
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Affiliation(s)
- Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itay Mayrose
- Department Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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193
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Balao F, Trucchi E, Wolfe TM, Hao B, Lorenzo MT, Baar J, Sedman L, Kosiol C, Amman F, Chase MW, Hedrén M, Paun O. Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima. Mol Ecol 2017; 26:3649-3662. [PMID: 28370647 PMCID: PMC5518283 DOI: 10.1111/mec.14123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 02/24/2017] [Accepted: 03/15/2017] [Indexed: 12/23/2022]
Abstract
The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.
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Affiliation(s)
- Francisco Balao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biología Vegetal y EcologíaUniversity of SevilleSevillaSpain
| | - Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Department of Life Sciences and BiotechnologiesUniversity of FerraraFerraraItaly
| | - Thomas M. Wolfe
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Bao‐Hai Hao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Maria Teresa Lorenzo
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biología Vegetal y EcologíaUniversity of SevilleSevillaSpain
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Laura Sedman
- Gregor Mendel Institute for Plant Molecular BiologyViennaAustria
| | - Carolin Kosiol
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Centre of Biological DiversitySchool of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Fabian Amman
- Department of Chromosome BiologyUniversity of ViennaViennaAustria
| | - Mark W. Chase
- Royal Botanic Gardens KewRichmondUK
- School of Plant BiologyUniversity of Western AustraliaCrawley, PerthWAAustralia
| | | | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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194
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Pérez‐Escobar OA, Chomicki G, Condamine FL, Karremans AP, Bogarín D, Matzke NJ, Silvestro D, Antonelli A. Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot. THE NEW PHYTOLOGIST 2017; 215:891-905. [PMID: 28631324 PMCID: PMC5575461 DOI: 10.1111/nph.14629] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/07/2017] [Indexed: 05/07/2023]
Abstract
The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with c. 15% of the world's plant species, in only 1% of the world's land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification. We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets. We find that the majority of Andean orchid lineages only originated in the last 20-15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones.
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Affiliation(s)
| | - Guillaume Chomicki
- Systematic Botany and MycologyUniversity of Munich (LMU)67 Menzinger Str.Munich80638Germany
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier)Place Eugène Bataillon34095MontpellierFrance
| | - Adam P. Karremans
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Diego Bogarín
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and GeneticsResearch School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Daniele Silvestro
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Department of Computational Biology, BiophoreUniversity of Lausanne1015LausanneSwitzerland
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
- Gothenburg Botanical GardenCarl Skottsbergs gata 22A41319GothenburgSweden
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195
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Niu SC, Huang J, Zhang YQ, Li PX, Zhang GQ, Xu Q, Chen LJ, Wang JY, Luo YB, Liu ZJ. Lack of S-RNase-Based Gametophytic Self-Incompatibility in Orchids Suggests That This System Evolved after the Monocot-Eudicot Split. FRONTIERS IN PLANT SCIENCE 2017; 8:1106. [PMID: 28690630 PMCID: PMC5479900 DOI: 10.3389/fpls.2017.01106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/07/2017] [Indexed: 05/25/2023]
Abstract
Self-incompatibility (SI) is found in approximately 40% of flowering plant species and at least 100 families. Although orchids belong to the largest angiosperm family, only 10% of orchid species present SI and have gametophytic SI (GSI). Furthermore, a majority (72%) of Dendrobium species, which constitute one of the largest Orchidaceae genera, show SI and have GSI. However, nothing is known about the molecular mechanism of GSI. The S-determinants of GSI have been well characterized at the molecular level in Solanaceae, Rosaceae, and Plantaginaceae, which use an S-ribonuclease (S-RNase)-based system. Here, we investigate the hypothesis that Orchidaceae uses a similar S-RNase to those described in Rosaceae, Solanaceae, and Plantaginaceae SI species. In this study, two SI species (Dendrobium longicornu and D. chrysanthum) were identified using fluorescence microscopy. Then, the S-RNase- and SLF-interacting SKP1-like1 (SSK1)-like genes present in their transcriptomes and the genomes of Phalaenopsis equestris, D. catenatum, Vanilla shenzhenica, and Apostasia shenzhenica were investigated. Sequence, phylogenetic, and tissue-specific expression analyses revealed that none of the genes identified was an S-determinant, suggesting that Orchidaceae might have a novel SI mechanism. The results also suggested that RNase-based GSI might have evolved after the split of monocotyledons (monocots) and dicotyledons (dicots) but before the split of Asteridae and Rosidae. This is also the first study to investigate S-RNase-based GSI in monocots. However, studies on gene identification, differential expression, and segregation analyses in controlled crosses are needed to further evaluate the genes with high expression levels in GSI tissues.
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Affiliation(s)
- Shan-Ce Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Graduate University of the Chinese Academy of SciencesBeijing, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Jie Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Pei-Xing Li
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of ShenzhenShenzhen, China
- The Centre for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangzhou, China
- College of Arts, College of Landscape Architecture, Fujian Agriculture and Forestry UniversityFuzhou, China
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196
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Nakamura A, Kitching RL, Cao M, Creedy TJ, Fayle TM, Freiberg M, Hewitt C, Itioka T, Koh LP, Ma K, Malhi Y, Mitchell A, Novotny V, Ozanne CM, Song L, Wang H, Ashton LA. Forests and Their Canopies: Achievements and Horizons in Canopy Science. Trends Ecol Evol 2017; 32:438-451. [DOI: 10.1016/j.tree.2017.02.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/21/2017] [Accepted: 02/24/2017] [Indexed: 11/26/2022]
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197
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Kolanowska M, Grochocka E, Konowalik K. Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives. PeerJ 2017; 5:e3328. [PMID: 28533976 PMCID: PMC5436590 DOI: 10.7717/peerj.3328] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 04/18/2017] [Indexed: 01/22/2023] Open
Abstract
In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids (Campylocentrum and Dendrophylax) and their closest relatives in the Old World (Angraecum) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae. No correlation between preferred niches and taxonomic relationships within the orchid group studied was revealed. The climatic suitability of the majority of the species overlapped each other, either fully or partially. This pattern is also present in the species of other orchid genera. Our research confirms a significant level of PNC in Orchidaceae, even within taxa exhibiting a transatlantic disjunction. The analysis of the evolution of climatic suitability indicated that the adaptation to various climatic conditions is not a factor that has driven speciation within orchids studied.
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Affiliation(s)
- Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Gdańsk, Poland.,Department of Biodiversity Research, Global Change Research Institute AS CR, Brno, Czech Republic
| | - Elżbieta Grochocka
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Gdańsk, Poland
| | - Kamil Konowalik
- Institute of Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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Niu Z, Xue Q, Zhu S, Sun J, Liu W, Ding X. The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots. FRONTIERS IN PLANT SCIENCE 2017; 8:715. [PMID: 28515737 PMCID: PMC5413554 DOI: 10.3389/fpls.2017.00715] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/18/2017] [Indexed: 05/20/2023]
Abstract
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5'trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic.
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Affiliation(s)
| | | | | | | | | | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal UniversityNanjing, China
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Laurent S, Salamin N, Robinson-Rechavi M. No evidence for the radiation time lag model after whole genome duplications in Teleostei. PLoS One 2017; 12:e0176384. [PMID: 28426792 PMCID: PMC5398669 DOI: 10.1371/journal.pone.0176384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the species richness of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of new phenotypic traits, although the radiation of the lineage would not occur before a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed increase of the species number after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to taxonomic diversity in teleosts.
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Affiliation(s)
- Sacha Laurent
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Abstract
Succulent plants are iconic components of the florae of many terrestrial ecosystems, but despite having caused fascination and prompted investigation for centuries, they still harbour many secrets in terms of physiological function and evolution. Tackling these mysteries is important, as this will not only provide insights into the dynamics and details of the convergent evolution of a major adaptive syndrome, but also inform efforts to conserve endangered biodiversity and utilize the unique physiological characteristics of succulents for biofuel and biomass production. Here I review advances in the phylogeny and organismal biology of succulent plants, and discuss how insights from recent work in the wider fields of plant hydraulics and photosynthetic physiology may relate to succulents. The potential for the exploration of mechanistic relationships between anatomical structure and physiological function to improve our understanding of the constraints that have shaped the evolution of succulence is highlighted. Finally, attention is drawn to how new methodologies and technologies provide exciting opportunities to address the wide range of outstanding questions in succulent plant biology.
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Affiliation(s)
- Jamie Males
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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