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Yagi R, Haraguchi TF, Tayasu I, Suetsugu K. Do exchangeable hydrogens affect the evaluation of partial mycoheterotrophy in orchids? Insights from δ 2H analysis in bulk, α-cellulose, and cellulose nitrate samples. THE NEW PHYTOLOGIST 2024; 243:2430-2441. [PMID: 39081019 DOI: 10.1111/nph.19998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/03/2024] [Indexed: 08/23/2024]
Abstract
To evaluate the nutritional modes of orchids associated with 'rhizoctonia' fungi, analyses of hydrogen (δ2H), carbon (δ13C), and nitrogen (δ15N) stable isotope ratios are usually adopted. However, previous studies have not fully accounted for exchangeable hydrogens, which could affect these evaluations. Here, we performed standard δ13C, δ15N, and δ2H analyses on bulk samples. Additionally, we conducted δ2H analysis on α-cellulose and cellulose nitrate samples to investigate whether the heterogeneity of exchangeable hydrogens among plant species influences the assessment of nutritional modes. The δ2H of orchids were consistently higher than those of surrounding autotrophic plants, irrespective of the three pretreatments. Although the rhizoctonia-associated orchid exhibited lower δ13C, its δ2H was higher than those of the autotrophs. Notably, among all response variables, δ15N and δ2H exhibited high abilities for discriminating the nutritional modes of rhizoctonia-associated orchids. These results indicate that a time-efficient bulk sample analysis is an effective method for evaluating plant nutritional modes, as the heterogeneity of exchangeable hydrogens does not significantly impact the estimation. Using δ15N and δ2H benefits the assessment of partial mycoheterotrophy among rhizoctonia-associated orchids.
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Affiliation(s)
- Ryuta Yagi
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Takashi F Haraguchi
- Biodiversity Research Center, Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 10-4 Koyamotomachi, Neyagawa, Osaka, 572-0088, Japan
| | - Ichiro Tayasu
- Research Institute of Humanity and Nature, 457-4, Motoyama, Kamigamo, Kyoto, 603-8047, Japan
| | - Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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Manyatsi TS, Lin YH, Sung PH, Jou YT. Exploring the Volatile Profile of Vanilla planifolia after Fermentation at Low Temperature with Bacillus Isolates. Foods 2024; 13:2777. [PMID: 39272542 PMCID: PMC11394893 DOI: 10.3390/foods13172777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Vanilla planifolia is grown as a high-value orchid spice for its odor and savor attributes that increase due to the curing process associated with microbial colonization. This tends to influence the aromatic properties of vanilla. Hence, 11 Bacillus sp. strains were isolated from V. planifolia and identified with 16S rRNA gene sequencing. The liquid culture (1 mL of 107 CFU mL-1) of selected Bacillus vallismortis NR_104873.1:11-1518, Bacillus velezensis ZN-S10, and Bacillus tropicus KhEp-2 effectively fermented green-blanched vanilla pods kept at 10 °C during the sweating stage. GC-MS analysis showed that the methanol extract of non-coated, and B. vallismortis treated vanilla detected three (3) volatile compounds, whereas seven (7) components were obtained in B. tropicus and B. velezensis treatment. 4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl was found in B. velezensis ZN-S10, B. tropicus KhEp-2, and B. vallismortis while it was not present in the control samples. This ketone compound suggested a Maillard reaction resulting in brown-increased aroma pods. Linoleic acid and Hexadecanoic acid ethyl esters were detected only in ZN-S10 strain-coated vanilla. A novel 3-Deoxy-d-mannoic lactone was detected only in B. vallismortis-treated vanilla characterized as a new compound in V. planifolia which suggested that the new compound can be altered with the coating of bacteria in vanilla during fermentation. Thus, the Bacillus strains improved the volatile profile and exhibited a new aroma and flavor profile of vanilla owing to bacteria fermentation during the curing process.
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Affiliation(s)
- Thabani-Sydney Manyatsi
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, Pingtung 91201, Taiwan
| | - Yu-Hsin Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, Pingtung 91201, Taiwan
| | - Pin-Hui Sung
- Kaohsiung District Agricultural Research and Extension Station, Ministry of Agriculture, Dehe Road 2-6, Pingtung 90846, Taiwan
| | - Ying-Tzy Jou
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, Pingtung 91201, Taiwan
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Stryker J, White E, Díaz-Almeyda E, Sidoti B, Oberle B. Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria. AMERICAN JOURNAL OF BOTANY 2024:e16396. [PMID: 39187952 DOI: 10.1002/ajb2.16396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]
Abstract
PREMISE Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity. METHODS We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata. RESULTS Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19 cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank. CONCLUSIONS Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.
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Affiliation(s)
- Jade Stryker
- New College of Florida, 5800 Bay Shore Road, Sarasota, 34243, FL, USA
| | - Elizabeth White
- New College of Florida, 5800 Bay Shore Road, Sarasota, 34243, FL, USA
- University of Florida, 3215 Hull Road, Gainesville, 32611, FL, USA
| | - Erika Díaz-Almeyda
- New College of Florida, 5800 Bay Shore Road, Sarasota, 34243, FL, USA
- California State University San Marcos, 333 South Twin Oaks Valley Road, San Marcos, 92096, CA, USA
| | - Brian Sidoti
- Kampong of The National Tropical Botanical Garden, 4013 South Douglas Road, Miami, 33133, FL, USA
| | - Brad Oberle
- New College of Florida, 5800 Bay Shore Road, Sarasota, 34243, FL, USA
- Marie Selby Botanical Garden, 1534 Mound Street, Sarasota, 34236, FL, USA
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, 10458, NY, USA
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Veltman MA, Anthoons B, Schrøder-Nielsen A, Gravendeel B, de Boer HJ. Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids. Mol Ecol Resour 2024; 24:e13986. [PMID: 38899721 DOI: 10.1111/1755-0998.13986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.
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Affiliation(s)
- Margaretha A Veltman
- Natural History Museum, Oslo, Norway
- Naturalis Biodiversity Center, Leiden, Netherlands
| | | | | | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden, Netherlands
- Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
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Barrett CF, Pace MC, Corbett CW. Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera. AMERICAN JOURNAL OF BOTANY 2024; 111:e16370. [PMID: 38989916 DOI: 10.1002/ajb2.16370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 07/12/2024]
Abstract
PREMISE Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. METHODS Using floral tissue from an herbarium specimen, we sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. RESULTS The plastome is the most reduced of those sequenced among the orchid subfamily Orchidoideae. In Degranvillea, it has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and of correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. CONCLUSIONS Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.
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Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
| | - Matthew C Pace
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, 10458, NY, USA
| | - Cameron W Corbett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
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Goedderz S, Clements MA, Bent SJ, Nicholls JA, Patel VS, Crayn DM, Schlüter PM, Nargar K. Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus Dipodium and provides insights into plastid gene degeneration. FRONTIERS IN PLANT SCIENCE 2024; 15:1388537. [PMID: 38938632 PMCID: PMC11210000 DOI: 10.3389/fpls.2024.1388537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. Leopardanthus is the sister lineage to sect. Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect. Dipodium, was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.
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Affiliation(s)
- Stephanie Goedderz
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Stephen J. Bent
- Data61, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - James A. Nicholls
- Australian National Insect Collection, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Vidushi S. Patel
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Darren M. Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Philipp M. Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
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Chen JC, Lin HY, Novák O, Strnad M, Lee YI, Fang SC. Diverse geotropic responses in the orchid family. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38809156 DOI: 10.1111/pce.14975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
In epiphytes, aerial roots are important to combat water-deficient, nutrient-poor, and high-irradiance microhabitats. However, whether aerial roots can respond to gravity and whether auxin plays a role in regulating aerial root development remain open-ended questions. Here, we investigated the gravitropic response of the epiphytic orchid Phalaenopsis aphrodite. Our data showed that aerial roots of P. aphrodite failed to respond to gravity, and this was correlated with a lack of starch granules/statolith sedimentation in the roots and the absence of the auxin efflux carrier PIN2 gene. Using an established auxin reporter, we discovered that auxin maximum was absent in the quiescent center of aerial roots of P. aphrodite. Also, gravity failed to trigger auxin redistribution in the root caps. Hence, loss of gravity sensing and gravity-dependent auxin redistribution may be the genetic factors contributing to aerial root development. Moreover, the architectural and functional innovations that achieve fast gravitropism in the flowering plants appear to be lost in both terrestrial and epiphytic orchids, but are present in the early diverged orchid subfamilies. Taken together, our findings provide physiological and molecular evidence to support the notion that epiphytic orchids lack gravitropism and suggest diverse geotropic responses in the orchid family.
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Affiliation(s)
- Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Simpson L, Clements MA, Orel HK, Crayn DM, Nargar K. Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum. FRONTIERS IN PLANT SCIENCE 2024; 14:1219354. [PMID: 38854888 PMCID: PMC11157511 DOI: 10.3389/fpls.2023.1219354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 06/11/2024]
Abstract
The hyperdiverse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only Bulbophyllum section with a center of diversity in Australasia is sect. Adelopetalum. However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within Bulbophyllum, and interspecific relationships within sect. Adelopetalum, a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (matK and ycf1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum, including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres, and Sestochilos. Section Adelopetalum and sect. Minutissima s.s. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the Early Oligocene (ca. 33.2 Ma) and sect. Adelopetalum in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. Adelopetalum. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. Adelopetalum facilitating allopatric speciation.
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Affiliation(s)
- Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and Commonwealth Industrial and Scientific Research Organisation (CSIRO)), Canberra, ACT, Australia
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Darren M. Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
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Silva FLD, de Medeiros BAS, Farrell BD. Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Mol Phylogenet Evol 2024; 194:108025. [PMID: 38342160 DOI: 10.1016/j.ympev.2024.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.
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Affiliation(s)
- Fabio Laurindo da Silva
- Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA.
| | - Bruno A S de Medeiros
- Field Museum of Natural History, Negaunee Integrative Research Center, Chicago, USA; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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Pérez-Escobar OA, Bogarín D, Przelomska NAS, Ackerman JD, Balbuena JA, Bellot S, Bühlmann RP, Cabrera B, Cano JA, Charitonidou M, Chomicki G, Clements MA, Cribb P, Fernández M, Flanagan NS, Gravendeel B, Hágsater E, Halley JM, Hu AQ, Jaramillo C, Mauad AV, Maurin O, Müntz R, Leitch IJ, Li L, Negrão R, Oses L, Phillips C, Rincon M, Salazar GA, Simpson L, Smidt E, Solano-Gomez R, Parra-Sánchez E, Tremblay RL, van den Berg C, Tamayo BSV, Zuluaga A, Zuntini AR, Chase MW, Fay MF, Condamine FL, Forest F, Nargar K, Renner SS, Baker WJ, Antonelli A. The origin and speciation of orchids. THE NEW PHYTOLOGIST 2024; 242:700-716. [PMID: 38382573 DOI: 10.1111/nph.19580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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Affiliation(s)
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
- Naturalis Biodiversity Centre, Leiden, CR 2333, the Netherlands
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - James D Ackerman
- University of Puerto Rico - Rio Piedras, San Juan, PR, 00925-2537, USA
| | | | | | | | - Betsaida Cabrera
- Jardín Botánico Rafael Maria Moscoso, Santo Domingo, 21-9, Dominican Republic
| | | | | | | | - Mark A Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Melania Fernández
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Nicola S Flanagan
- Universidad Pontificia Javeriana, Seccional Cali, Cali, 760031, Colombia
| | | | | | | | - Ai-Qun Hu
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 257494, Singapore
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Apartado, Panama City, 0843-03092, Panama
| | | | | | - Robert Müntz
- Reserva Biológica Guaitil, Eisenstadt, 7000, Austria
| | | | - Lan Li
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lizbeth Oses
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Charlotte Phillips
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Milton Rincon
- Jardín Botánico Jose Celestino Mutis, Bogota, 111071, Colombia
| | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
| | - Eric Smidt
- Universidade Federal do Paraná, Curitiba, 19031, Brazil
| | | | | | | | - Cassio van den Berg
- Universidade Estadual de Feira de Santana, Feira de Santana, 44036-900, Brazil
| | | | | | | | - Mark W Chase
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | | | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugène Bataillon, Montpellier, 34000, France
| | | | - Katharina Nargar
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
- Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, 417 56, Sweden
- University of Gothenburg, Gothenburg, 417 56, Sweden
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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12
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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Zhang MM, Zhao X, He X, Zheng Q, Huang Y, Li Y, Ke S, Liu ZJ, Lan S. Genome-Wide Identification of PEBP Gene Family in Two Dendrobium Species and Expression Patterns in Dendrobium chrysotoxum. Int J Mol Sci 2023; 24:17463. [PMID: 38139293 PMCID: PMC10743876 DOI: 10.3390/ijms242417463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
The PEBP gene family plays a significant role in regulating flower development and formation. To understand its function in Dendrobium chrysotoxum and D. nobile flowering, we identified 22 PEBP genes (11 DchPEBPs and 11 DnoPEBPs) from both species. We conducted analyses on their conserved domains and motifs, phylogenetic relationships, chromosome distribution, collinear correlation, and cis elements. The classification results showed that the 22 PEBPs were mainly divided into three clades, as follows: FT, MFT, and TFL1. A sequence analysis showed that most PEBP proteins contained five conserved domains, while a gene structure analysis revealed that 77% of the total PEBP genes contained four exons and three introns. The promoter regions of the 22 PEBPs contained several cis elements related to hormone induction and light response. This suggests these PEBPs could play a role in regulating flower development by controlling photoperiod and hormone levels. Additionally, a collinearity analysis revealed three pairs of duplicate genes in the genomes of both D. chrysotoxum and D. nobile. Furthermore, RT-qPCR has found to influence the regulatory effect of DchPEBPs on the development of flower organs (sepals, petals, lip, ovary, and gynostemium) during the flowering process (bud, transparent stage, and initial bloom). The results obtained imply that DchPEBP8 and DchPEBP9 play a role in the initial bloom and that DchPEBP7 may inhibit flowering processes. Moreover, DchPEBP9 may potentially be involved in the development of reproductive functionality. PEBPs have regulatory functions that modulate flowering. FT initiates plant flowering by mediating photoperiod and temperature signals, while TFL1 inhibits flowering processes. These findings provide clues for future studies on flower development in Dendrobium.
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Affiliation(s)
- Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.Z.); (X.H.); (S.K.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.H.); (Y.L.)
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15
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Liu DK, Zhou CY, Tu XD, Zhao Z, Chen JL, Gao XY, Xu SW, Zeng MY, Ma L, Ahmad S, Li MH, Lan S, Liu ZJ. Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes. BMC Genomics 2023; 24:749. [PMID: 38057701 DOI: 10.1186/s12864-023-09847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. RESULTS We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA > psbK-psbI > psaC-rps15 > trnEUUC-trnTGGU > accD-psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support. CONCLUSION This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.
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Affiliation(s)
- Ding-Kun Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuang Zhao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin-Liao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu-Yong Gao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shao-Wei Xu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liang Ma
- Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Sagheer Ahmad
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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16
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Zotz G, Andrade JL, Einzmann HJR. CAM plants: their importance in epiphyte communities and prospects with global change. ANNALS OF BOTANY 2023; 132:685-698. [PMID: 36617243 PMCID: PMC10799991 DOI: 10.1093/aob/mcac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND SCOPE The epiphytic life form characterizes almost 10 % of all vascular plants. Defined by structural dependence throughout their life and their non-parasitic relationship with the host, the term epiphyte describes a heterogeneous and taxonomically diverse group of plants. This article reviews the importance of crassulacean acid metabolism (CAM) among epiphytes in current climatic conditions and explores the prospects under global change. RESULTS AND CONCLUSIONS We question the view of a disproportionate importance of CAM among epiphytes and its role as a 'key innovation' for epiphytism but do identify ecological conditions in which epiphytic existence seems to be contingent on the presence of this photosynthetic pathway. Possibly divergent responses of CAM and C3 epiphytes to future changes in climate and land use are discussed with the help of experimental evidence, current distributional patterns and the results of several long-term descriptive community studies. The results and their interpretation aim to stimulate a fruitful discussion on the role of CAM in epiphytes in current climatic conditions and in altered climatic conditions in the future.
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Affiliation(s)
- Gerhard Zotz
- Functional Ecology Group, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Box 5634, D-26046 Oldenburg, Germany
- Smithsonian Tropical Research Institute, Box 0843-03092, Panama, Republic of Panama
| | - José Luis Andrade
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - Helena J R Einzmann
- Functional Ecology Group, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Box 5634, D-26046 Oldenburg, Germany
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17
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Gilman IS, Smith JAC, Holtum JAM, Sage RF, Silvera K, Winter K, Edwards EJ. The CAM lineages of planet Earth. ANNALS OF BOTANY 2023; 132:627-654. [PMID: 37698538 PMCID: PMC10799995 DOI: 10.1093/aob/mcad135] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/09/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND AND SCOPE The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages. RESULTS AND CONCLUSIONS We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.
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Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katia Silvera
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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18
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Sage RF, Gilman IS, Smith JAC, Silvera K, Edwards EJ. Atmospheric CO2 decline and the timing of CAM plant evolution. ANNALS OF BOTANY 2023; 132:753-770. [PMID: 37642245 PMCID: PMC10799994 DOI: 10.1093/aob/mcad122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/19/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS CAM photosynthesis is hypothesized to have evolved in atmospheres of low CO2 concentration in recent geological time because of its ability to concentrate CO2 around Rubisco and boost water use efficiency relative to C3 photosynthesis. We assess this hypothesis by compiling estimates of when CAM clades arose using phylogenetic chronograms for 73 CAM clades. We further consider evidence of how atmospheric CO2 affects CAM relative to C3 photosynthesis. RESULTS Where CAM origins can be inferred, strong CAM is estimated to have appeared in the past 30 million years in 46 of 48 examined clades, after atmospheric CO2 had declined from high (near 800 ppm) to lower (<450 ppm) values. In turn, 21 of 25 clades containing CAM species (but where CAM origins are less certain) also arose in the past 30 million years. In these clades, CAM is probably younger than the clade origin. We found evidence for repeated weak CAM evolution during the higher CO2 conditions before 30 million years ago, and possible strong CAM origins in the Crassulaceae during the Cretaceous period prior to atmospheric CO2 decline. Most CAM-specific clades arose in the past 15 million years, in a similar pattern observed for origins of C4 clades. CONCLUSIONS The evidence indicates strong CAM repeatedly evolved in reduced CO2 conditions of the past 30 million years. Weaker CAM can pre-date low CO2 and, in the Crassulaceae, strong CAM may also have arisen in water-limited microsites under relatively high CO2. Experimental evidence from extant CAM species demonstrates that elevated CO2 reduces the importance of nocturnal CO2 fixation by increasing the contribution of C3 photosynthesis to daily carbon gain. Thus, the advantage of strong CAM would be reduced in high CO2, such that its evolution appears less likely and restricted to more extreme environments than possible in low CO2.
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Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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19
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Rammitsu K, Goto M, Yamashita Y, Yukawa T, Ogura-Tsujita Y. Mycorrhizal specificity differences in epiphytic habitat: three epiphytic orchids harbor distinct ecological and physiological specificity. JOURNAL OF PLANT RESEARCH 2023; 136:803-816. [PMID: 37572242 DOI: 10.1007/s10265-023-01486-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/26/2023] [Indexed: 08/14/2023]
Abstract
Orchidaceae has diversified in tree canopies and accounts for 68% of vascular epiphytes. Differences in mycorrhizal communities among epiphytic orchids can reduce species competition for mycorrhizal fungi and contribute to niche partitioning, which may be a crucial driver of the unusual species diversification among orchids. Mycorrhizal specificity-the range of fungi allowing mycorrhizal partnerships-was evaluated by assessment of mycorrhizal communities in the field (ecological specificity) and symbiotic cultures in the laboratory (physiological specificity) for three epiphytic orchids inhabiting Japan. Mycorrhizal communities were assessed with co-existing individuals growing within 10 cm of each other, revealing that ecological specificity varied widely among the three species, ranging from dominance by a single Ceratobasidiaceae fungus to diverse mycobionts across the Ceratobasidiaceae and Tulasnellaceae. In vitro seed germination tests revealed clear differences in physiological specificity among the three orchids, and that the primary mycorrhizal partners contributed to seed germination. In vitro compatibility ranges of three orchids strongly reflect the mycorrhizal community composition of wild populations. This suggests that differences in in situ mycorrhizal communities are not strongly driven by environmental factors, but are primarily due to physiological differences among orchid species. This study shows that the symbiotic strategy among the epiphytic orchid species varies from specialized to generalized association, which may contribute to biotic niche partitioning.
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Affiliation(s)
- Kento Rammitsu
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masaru Goto
- Shizuoka Calanthe Society, Fujishi, Shizuoka, Japan
| | - Yumi Yamashita
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, Fukushima, Japan
| | - Tomohisa Yukawa
- National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Yuki Ogura-Tsujita
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Faculty of Agriculture, Saga University, Saga, Japan.
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20
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Ning HJ, Gui FF, Tian EW, Yang LY. The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium. BMC PLANT BIOLOGY 2023; 23:492. [PMID: 37833649 PMCID: PMC10571305 DOI: 10.1186/s12870-023-04499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis. RESULT In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses. CONCLUSION In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.
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Affiliation(s)
- Hui-Juan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Fang-Fang Gui
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - En-Wei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Li-Yuan Yang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou, 311300, Zhejiang, China.
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21
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Soghigian J, Sither C, Justi SA, Morinaga G, Cassel BK, Vitek CJ, Livdahl T, Xia S, Gloria-Soria A, Powell JR, Zavortink T, Hardy CM, Burkett-Cadena ND, Reeves LE, Wilkerson RC, Dunn RR, Yeates DK, Sallum MA, Byrd BD, Trautwein MD, Linton YM, Reiskind MH, Wiegmann BM. Phylogenomics reveals the history of host use in mosquitoes. Nat Commun 2023; 14:6252. [PMID: 37803007 PMCID: PMC10558525 DOI: 10.1038/s41467-023-41764-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023] Open
Abstract
Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188-250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.
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Affiliation(s)
- John Soghigian
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Charles Sither
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Gen Morinaga
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Brian K Cassel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Christopher J Vitek
- Center for Vector-Borne Diseases, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Todd Livdahl
- Department of Biology, Clark University, Worcester, MA, USA
| | - Siyang Xia
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thomas Zavortink
- Bohart Museum of Entomology, University of California, Davis, CA, USA
| | | | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Lawrence E Reeves
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Richard C Wilkerson
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Collections and Marine Infrastructure, Canberra, ACT, Australia
| | - Maria Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saude Publica, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Brian D Byrd
- College of Health and Human Sciences, School of Health Sciences, Western Carolina University, Cullowhee, NC, USA
| | - Michelle D Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Michael H Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Brian M Wiegmann
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
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22
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Wang X, Peng P, Bai M, Bai W, Zhang S, Feng Y, Wang J, Tang Y. Impacts of physiological characteristics and human activities on the species distribution models of orchids taking the Hengduan Mountains as a case. Ecol Evol 2023; 13:e10566. [PMID: 37791293 PMCID: PMC10542477 DOI: 10.1002/ece3.10566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
The biogeography research of orchids through species distribution models (SDMs), a vital tool in the biogeography field, is critical to understanding the fundamental geographic distribution patterns and identifying conservation priorities. The correspondence between species occurrence and environmental information is crucial to the model's performance. However, ecological preferences unique to different orchid species, such as their life forms, are often overlooked during the modeling process. This oversight can introduce bias and increase model uncertainty. Additionally, human activities, as an important potential predictor, have not been quantified in any orchid SDMs. Taking the Hengduan Mountains as an example, we preprocessed all orchid species' occurrences based on physiological characteristics. Choosing five spatial factors related to human activities to quantify the interference and enter into models as HI factor. Using different modeling methods (GLM, MaxEnt, and RF) and evaluation indices (AUC, TSS, and Kappa), diverse modeling strategies have been constructed in the study. A double-ranking method has been adopted to select the critical orchid distribution regions. The results showed that classification models based on physiological characteristics significantly improved the model's accuracy while adding the HI factor had the same effect but the absence of enough significance. Suitability maps indicated that highly heterogeneous mountainous areas were vital for the distribution of orchids in the Hengduan Mountains. Different distribution patterns and critical regions existed between various orchid life forms geographically - terrestrial orchids were dominant in the mountain, and mycoherterophical orchids were primarily located in the north, more influenced by vegetation and temperature. Critical regions of epiphytic orchids were in the south due to a greater dependence on precipitation and temperature. These studies are informative for understanding the orchids' geographic distribution patterns in the Hengduan Mountains, promoting conservation and providing references for similar research beyond orchids.
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Affiliation(s)
- Xue‐Man Wang
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Pei‐Hao Peng
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Mao‐Yang Bai
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Wen‐Qian Bai
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Shi‐Qi Zhang
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Yu Feng
- College of Earth SciencesChengdu University of TechnologyChengduChina
| | - Juan Wang
- College of Tourism and Urban‐rural PlanningChengdu University of TechnologyChengduChina
| | - Ying Tang
- College of Tourism and Urban‐rural PlanningChengdu University of TechnologyChengduChina
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23
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Zhao Z, Zeng MY, Wu YW, Li JW, Zhou Z, Liu ZJ, Li MH. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. Int J Mol Sci 2023; 24:14437. [PMID: 37833887 PMCID: PMC10572996 DOI: 10.3390/ijms241914437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.
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Affiliation(s)
- Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Yu-Wei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Jin-Wei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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24
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Kriebel R, Rose JP, Bastide P, Jolles D, Reginato M, Sytsma KJ. The evolution of Ericaceae flowers and their pollination syndromes at a global scale. AMERICAN JOURNAL OF BOTANY 2023; 110:e16220. [PMID: 37551426 DOI: 10.1002/ajb2.16220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Floral evolution in large clades is difficult to study not only because of the number of species involved, but also because they often are geographically widespread and include a diversity of outcrossing pollination systems. The cosmopolitan blueberry family (Ericaceae) is one such example, most notably pollinated by bees and multiple clades of nectarivorous birds. METHODS We combined data on floral traits, pollination ecology, and geography with a comprehensive phylogeny to examine the structuring of floral diversity across pollination systems and continents. We focused on ornithophilous systems to test the hypothesis that some Old World Ericaceae were pollinated by now-extinct hummingbirds. RESULTS Despite some support for floral differentiation at a continental scale, we found a large amount of variability within and among landmasses, due to both phylogenetic conservatism and parallel evolution. We found support for floral differentiation in anther and corolla traits across pollination systems, including among different ornithophilous systems. Corolla traits show inconclusive evidence that some Old World Ericaceae were pollinated by hummingbirds, while anther traits show stronger evidence. Some major shifts in floral traits are associated with changes in pollination system, but shifts within bee systems are likely also important. CONCLUSIONS Studying the floral evolution of large, morphologically diverse, and widespread clades is feasible. We demonstrate that continent-specific radiations have led to widespread parallel evolution of floral morphology. We show that traits outside of the perianth may hold important clues to the ecological history of lineages.
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Affiliation(s)
- Ricardo Kriebel
- Department of Botany, California Academy of Sciences, San Francisco, California, 94118, USA
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Diana Jolles
- Department of Biological Sciences, Plymouth State University, 17 High Street, Plymouth, New Hampshire, 03264-1594, USA
| | - Marcelo Reginato
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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25
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Thompson JB, Davis KE, Dodd HO, Wills MA, Priest NK. Speciation across the Earth driven by global cooling in terrestrial orchids. Proc Natl Acad Sci U S A 2023; 120:e2102408120. [PMID: 37428929 PMCID: PMC10629580 DOI: 10.1073/pnas.2102408120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/03/2023] [Indexed: 07/12/2023] Open
Abstract
Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.
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Affiliation(s)
- Jamie B. Thompson
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Katie E. Davis
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | - Harry O. Dodd
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Matthew A. Wills
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Nicholas K. Priest
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
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26
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Kim YK, Jo S, Cheon SH, Hong JR, Kim KJ. Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). Int J Mol Sci 2023; 24:11448. [PMID: 37511216 PMCID: PMC10380568 DOI: 10.3390/ijms241411448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ja-Ram Hong
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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27
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Zhou P, Li JH, Liu YZ, Zhu ZW, Luo Y, Xiang XG. Species richness disparity in tropical terrestrial herbaceous floras: evolutionary insight from Collabieae (Orchidaceae). Mol Phylogenet Evol 2023:107860. [PMID: 37329932 DOI: 10.1016/j.ympev.2023.107860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
Species richness is spatially heterogeneous even in the hyperdiverse tropical floras. The main cause of uneven species richness among the four tropical regions are hot debated. To date, higher net diversification rates and/or longer colonization time have been usually proposed to contribute to this pattern. However, there are few studies to clarify the species richness patterns in tropical terrestrial floras. The terrestrial tribe Collabieae (Orchidaceae) unevenly distributes in the tropical regions with a diverse and endemic center in Asia. Twenty-one genera 127 species of Collabieae and 26 DNA regions were used to reconstruct the phylogeny and infer the biogeographical processes. We compared the topologies, diversification rates and niche rates of Collabieae and regional lineages on empirical samplings and different simulated samplings fractions respectively. Our results suggested that the Collabieae originated in Asia at the earliest Oligocene, and then independently spread to Africa, Central America, and Oceania since the Miocene via long-distance dispersal. These results based on empirical data and simulated data were similar. BAMM, GeoSSE and niche analyses inferred that the Asian lineages had higher net diversification and niche rates than those of Oceanian and African lineages on the empirical and simulated analyses. Precipitation is the most important factor for Collabieae, and the Asian lineage has experienced more stable and humid climate, which may promote the higher net diversification rate. Besides, the longer colonization time may also be associated with the Asian lineages' diversity. These findings provided a better understanding of the regional diversity heterogeneity in tropical terrestrial herbaceous floras.
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Affiliation(s)
- Peng Zhou
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Ji-Hong Li
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong, China
| | - Yi-Zhen Liu
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Zi-Wei Zhu
- Jiangxi Academy of Forest, Nanchang, Jiangxi, China
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China.
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Vitt P, Taylor A, Rakosy D, Kreft H, Meyer A, Weigelt P, Knight TM. Global conservation prioritization for the Orchidaceae. Sci Rep 2023; 13:6718. [PMID: 37185616 PMCID: PMC10130154 DOI: 10.1038/s41598-023-30177-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/17/2023] [Indexed: 05/17/2023] Open
Abstract
Quantitative assessments of endemism, evolutionary distinctiveness and extinction threat underpin global conservation prioritization for well-studied taxa, such as birds, mammals, and amphibians. However, such information is unavailable for most of the world's taxa. This is the case for the Orchidaceae, a hyperdiverse and cosmopolitan family with incomplete phylogenetic and threat information. To define conservation priorities, we present a framework based on phylogenetic and taxonomic measures of distinctiveness and rarity based on the number of regions and the area of occupancy. For 25,434 orchid species with distribution data (89.3% of the Orchidaceae), we identify the Neotropics as hotspots for richness, New Guinea as a hotspot for evolutionary distinctiveness, and several islands that contain many rare and distinct species. Orchids have a similar proportion of monotypic genera as other Angiosperms, however, more taxonomically distinct orchid species are found in a single region. We identify 278 species in need of immediate conservation actions and find that more than 70% of these do not currently have an IUCN conservation assessment and are not protected in ex-situ collections at Botanical Gardens. Our study highlights locations and orchid species in urgent need of conservation and demonstrates a framework that can be applied to other data-deficient taxa.
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Affiliation(s)
- Pati Vitt
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA.
- Plant Conservation and Biology, Northwestern University, Evanston, IL, 60203, USA.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
| | - Amanda Taylor
- Biodiversity, Macroecology & Biogeography, Faculty for Forest Sciences & Forest Ecology, Goettingen University, Buesgenweg 1, 37077, Göttingen, Germany
| | - Demetra Rakosy
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Department Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Straße4, 06120, Halle (Saale), Germany
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, Faculty for Forest Sciences & Forest Ecology, Goettingen University, Buesgenweg 1, 37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Abby Meyer
- Botanic Gardens Conservation International, U.S., 1151 Oxford Road, Botanical Division, San Marino, CA, 91108, USA
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography, Faculty for Forest Sciences & Forest Ecology, Goettingen University, Buesgenweg 1, 37077, Göttingen, Germany
- Campus-Institut Data Science, Göttingen, Germany
| | - Tiffany M Knight
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Department Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Straße4, 06120, Halle (Saale), Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle (Saale), Germany
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Xue Q, Yang J, Yu W, Wang H, Hou Z, Li C, Xue Q, Liu W, Ding X, Niu Z. The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways. BMC PLANT BIOLOGY 2023; 23:189. [PMID: 37038109 PMCID: PMC10084689 DOI: 10.1186/s12870-023-04186-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Dendrobium orchids have multiple photosynthetic pathways, which can be used as a model system for studying the evolution of crassulacean acid metabolism (CAM). In this study, based on the results of the net photosynthetic rates (Pn), we classified Dendrobium species into three photosynthetic pathways, then employed and compared their chloroplast genomes. The Dendrobium chloroplast genomes have typical quartile structures, ranging from 150,841-153,038 bp. The apparent differences in GC content, sequence variability, and IR junctions of SSC/IRB junctions (JSBs) were measured within chloroplast genomes among different photosynthetic pathways. The phylogenetic analysis has revealed multiple independent CAM origins among the selected Dendrobium species. After counting insertions and deletions (InDels), we found that the occurrence rates and distribution densities among different photosynthetic pathways were inconsistent. Moreover, the evolution patterns of chloroplast genes in Dendrobium among three photosynthetic pathways were also diversified. Considering the diversified genome structure variations and the evolution patterns of protein-coding genes among Dendrobium species, we proposed that the evolution of the chloroplast genomes was disproportional among different photosynthetic pathways. Furthermore, climatic correlation revealed that temperature and precipitation have influenced the distribution among different photosynthetic pathways and promoted the foundation of CAM pathway in Dendrobium orchids. Based on our study, we provided not only new insights into the CAM evolution of Dendrobium but also provided beneficial genetic data resources for the further systematical study of Dendrobium.
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Affiliation(s)
- Qiqian Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Hongman Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Zhenyu Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Chao Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
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Li X, Zhe M, Huang Y, Fan W, Yang J, Zhu A. The Evolution of Mitochondrial Genomes between Two Cymbidium Sister Species: Dozens of Circular Chromosomes and the Maintenance and Deterioration of Genome Synteny. Genes (Basel) 2023; 14:genes14040864. [PMID: 37107622 PMCID: PMC10137497 DOI: 10.3390/genes14040864] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy.
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Affiliation(s)
- Xiaoling Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Evans SA, Whigham DF, Hartvig I, McCormick MK. Hybridization in the Fringed Orchids: An Analysis of Species Boundaries in the Face of Gene Flow. DIVERSITY 2023. [DOI: 10.3390/d15030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts.
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Fernández M, Kaur J, Sharma J. Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny. MYCORRHIZA 2023; 33:87-105. [PMID: 36651985 DOI: 10.1007/s00572-022-01099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.
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Affiliation(s)
- Melania Fernández
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
- Lankester Botanical Garden, University of Costa Rica, Cartago, 30109, Costa Rica.
- Herbarium UCH, Universidad Autónoma de Chiriquí, David, Chiriquí, Panama.
| | - Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
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Pittermann J, Baer A, Campany C, Jansen S, Holmlund H, Schuettpelz E, Mehltreter K, Watkins JE. A reduced role for water transport during the Cenozoic evolution of epiphytic Eupolypod ferns. THE NEW PHYTOLOGIST 2023; 237:1745-1758. [PMID: 36484140 DOI: 10.1111/nph.18667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The Cretaceous-Cenozoic expansion of tropical forests created canopy space that was subsequently occupied by diverse epiphytic communities including Eupolypod ferns. Eupolypods proliferated in this more stressful niche, where lower competition enabled the adaptive radiation of thousands of species. Here, we examine whether xylem traits helped shape the Cenozoic radiation of Eupolypod ferns. We characterized the petiole xylem anatomy of 39 species belonging to the Eupolypod I and Eupolypod II clades occupying the epiphytic, hemiepiphytic, and terrestrial niche, and we assessed vulnerability to embolism in a subset of species. The transition to the canopy was associated with reduced xylem content and smaller tracheid diameters, but no differences were found in species vulnerability to embolism and pit membrane thickness. Phylogenetic analyses support selection for traits associated with reduced water transport in Eupolypod 1 species. We posit that in Eupolypod epiphytes, selection favored water retention via thicker leaves and lower stomatal density over higher rates of water transport. Consequently, lower leaf water loss was coupled with smaller quantities of xylem and narrower tracheid diameters. Traits associated with water conservation were evident in terrestrial Eupolypod 1 ferns and may have predisposed this clade toward radiation in the canopy.
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Affiliation(s)
- Jarmila Pittermann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Alex Baer
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Courtney Campany
- Department of Biology, Shepherd University, Shepherdstown, WV, 25443, USA
| | - Steven Jansen
- Institute for Systematic Botany and Ecology, University of Ulm, Ulm, 89081, Germany
| | - Helen Holmlund
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Klaus Mehltreter
- Red de Ecologia Funcíonal, Instituto de Ecología A.C, Xalapa, Veracruz, 91073, Mexico
| | - James E Watkins
- Department of Biology, Colgate University, Hamilton, NY, 13346, USA
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Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae). Int J Mol Sci 2023; 24:ijms24043808. [PMID: 36835219 PMCID: PMC9966724 DOI: 10.3390/ijms24043808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, and then the evolutionary patterns of plastomes were compared to all available vanilloid plastomes. Pogonia japonica has the longest plastome, with 158,200 bp in genome size. In contrast, Lecanorchis japonica has the shortest plastome with 70,498 bp in genome size. The vanilloid plastomes have regular quadripartite structures, but the small single copy (SSC) region was drastically reduced. Two different tribes of Vanilloideae (Pogonieae and Vanilleae) showed different levels of SSC reductions. In addition, various gene losses were observed among the vanilloid plastomes. The photosynthetic vanilloids (Pogonia and Vanilla) showed signs of stage 1 degradation and had lost most of their ndh genes. The other three species (one Cyrotsia and two Lecanorchis), however, had stage 3 or stage 4 degradation and had lost almost all the genes in their plastomes, except for some housekeeping genes. The Vanilloideae were located between the Apostasioideae and Cypripedioideae in the maximum likelihood tree. A total of ten rearrangements were found among ten Vanilloideae plastomes when compared to the basal Apostasioideae plastomes. The four sub-regions of the single copy (SC) region shifted into an inverted repeat (IR) region, and the other four sub-regions of the IR region shifted into the SC regions. Both the synonymous (dS) and nonsynonymous (dN) substitution rates of IR in-cooperated SC sub-regions were decelerated, while the substitution rates of SC in-cooperated IR sub-regions were accelerated. A total of 20 protein-coding genes remained in mycoheterotrophic vanilloids. Almost all these protein genes show accelerated base substitution rates compared to the photosynthetic vanilloids. Two of the twenty genes in the mycoheterotrophic species faced strong "relaxed selection" pressure (p-value < 0.05).
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Li Y, Chen X, Lin X, Gu Y, Liu B, Zhang R. Complete chloroplast genome of Isoetes orientalis (Isoetaceae), an endangered quillwort from China. Mitochondrial DNA B Resour 2023; 8:342-346. [PMID: 36876143 PMCID: PMC9980155 DOI: 10.1080/23802359.2023.2183070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Isoetes orientalis is an endangered hexaploidy species of Isoetaceae in China and the complete chloroplast genome of this species has not been reported. In the present study, a complete chloroplast genome of Isoetes orientalis (Isoetaceae) was assembled and annotated. This chloroplast genome has a circular structure of 145,504 bp in length, comprising a pair of inverted repeat (IR) regions of 13,207 bp each, a large single-copy (LSC) region of 91,864 bp, and a small single-copy (SSC) region of 27,226 bp. The chloroplast genome contains 136 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that I. orientalis was closely related to I. sinensis. These results provide additional resources for future studies on Isoetes from China and across the globe.
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Affiliation(s)
- Yanqing Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Xi Chen
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Xiaoyan Lin
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Yufeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation & Research Center of Shenzhen, Shenzhen, China.,Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Baodong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Rongjing Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Volatile Organic Compounds (VOCs) Diversity in the Orchid Himantoglossum robertianum (Loisel.) P. Delforge from Sardinia (Italy). DIVERSITY 2022. [DOI: 10.3390/d14121125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Volatile Organic Compounds (VOCs) are produced by plants to address a variety of physiological and ecological tasks (among others, stress resistance, and pollinator attraction). Genetics is a key factor in determining plants’ VOCs content and emission, nevertheless, environment strongly influences VOCs profiles in plants. Orchids are a widespread group of plants that colonize diverse environments and rely on complex and refined pollination mechanisms to reproduce. Orchids VOCs are rarely studied and discussed in relation to growing conditions. In the present study, we compare the volatile profiles of inflorescences of Himantoglossum robertianum (Loisel.) P. Delforge sampled in six ecologically diverse populations on Sardinia Island (Italy). The essential oils obtained by steam distillation were characterized by GC-FID and GC-MS analysis. A total of 79 compounds were detected, belonging to the chemical classes of saturated hydrocarbons, esters, alcohols, ketones, unsaturated hydrocarbons, sesquiterpenes, oxygenated terpenes, terpenes, acids, and aldehydes. Multivariate statistics separated H. robertianum populations based on their chemical profiles. Differences were positively linked to the distance separating populations and reflected climatological features of the sampling sites. Interestingly, our results differed from those available in the literature, pointing out the high variability of VOCs profiles in this food-deceptive orchid.
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Liu DK, Zhang C, Zhao X, Ke S, Li Y, Zhang D, Zheng Q, Li MH, Lan S, Liu ZJ. Genome-wide analysis of the TCP gene family and their expression pattern in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2022; 13:1068969. [PMID: 36570938 PMCID: PMC9772009 DOI: 10.3389/fpls.2022.1068969] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
TCP gene family are specific transcription factors for plant, and considered to play an important role in development and growth. However, few related studies investigated the TCP gene trait and how it plays a role in growth and development of Orchidaceae. In this study, we obtained 14 TCP genes (CgTCPs) from the Spring Orchid Cymbidium goeringii genome. The classification results showed that 14 CgTCPs were mainly divided into two clades as follows: four PCF genes (Class I), nine CIN genes and one CYC gene (Class II). The sequence analysis showed that the TCP proteins of C. goeringii contain four conserved regions (basic Helix-Loop-Helix) in the TCP domain. The exon-intron structure varied in the clade according to a comparative investigation of the gene structure, and some genes had no introns. There are fewer CgTCP homologous gene pairs compared with Dendrobium catenatum and Phalaenopsis equestris, suggesting that the TCP genes in C. goeringii suffered more loss events. The majority of the cis-elements revealed to be enriched in the function of light responsiveness, followed by MeJA and ABA responsiveness, demonstrating their functions in regulating by light and phytohormones. The collinearity study revealed that the TCPs in D. catenatum, P. equestris and C. goeringii almost 1:1. The transcriptomic data and real-time reverse transcription-quantitative PCR (RT-qPCR) expression profiles showed that the flower-specific expression of the TCP class II genes (CgCIN2, CgCIN5 and CgCIN6) may be related to the regulation of florescence. Altogether, this study provides a comprehensive analysis uncovering the underlying function of TCP genes in Orchidaceae.
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Affiliation(s)
- Ding-Kun Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-He Li
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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Klimpert NJ, Mayer JLS, Sarzi DS, Prosdocimi F, Pinheiro F, Graham SW. Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii. AMERICAN JOURNAL OF BOTANY 2022; 109:2030-2050. [PMID: 36254561 DOI: 10.1002/ajb2.16084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Pogoniopsis likely represents an independent photosynthesis loss in orchids. We use phylogenomic data to better identify the phylogenetic placement of this fully mycoheterotrophic taxon, and investigate its molecular evolution. METHODS We performed likelihood analysis of plastid and mitochondrial phylogenomic data to localize the position of Pogoniopsis schenckii in orchid phylogeny, and investigated the evolution of its plastid genome. RESULTS All analyses place Pogoniopsis in subfamily Epidendroideae, with strongest support from mitochondrial data, which also place it near tribe Sobralieae with moderately strong support. Extreme rate elevation in Pogoniopsis plastid genes broadly depresses branch support; in contrast, mitochondrial genes are only mildly rate elevated and display very modest and localized reductions in bootstrap support. Despite considerable genome reduction, including loss of photosynthesis genes and multiple translation apparatus genes, gene order in Pogoniopsis plastomes is identical to related autotrophs, apart from moderately shifted inverted repeat (IR) boundaries. All cis-spliced introns have been lost in retained genes. Two plastid genes (accD, rpl2) show significant strengthening of purifying selection. A retained plastid tRNA gene (trnE-UUC) of Pogoniopsis lacks an anticodon; we predict that it no longer functions in translation but retains a secondary role in heme biosynthesis. CONCLUSIONS Slowly evolving mitochondrial genes clarify the placement of Pogoniopsis in orchid phylogeny, a strong contrast with analysis of rate-elevated plastome data. We documented the effects of the novel loss of photosynthesis: for example, despite massive gene loss, its plastome is fully colinear with other orchids, and it displays only moderate shifts in selective pressure in retained genes.
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Affiliation(s)
- Nathaniel J Klimpert
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
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Yadav A, Mudoi KD, Kumar N, Geed SR, Gogoi P, Sharma RK, Saikia R. Auxin biosynthesis by Microbacterium testaceum Y411 associated with orchid aerial roots and their efficacy in micropropagation. FRONTIERS IN PLANT SCIENCE 2022; 13:1037109. [PMID: 36518501 PMCID: PMC9742431 DOI: 10.3389/fpls.2022.1037109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Root-associated bacteria strongly affect plant growth and development by synthesizing growth regulators and stress-relieving metabolites. The present study is mainly focused on assessing aerial root-associated bacteria of Rhynchostylis retusa (L.) Blume is an endemic epiphytic orchid responsible for auxin production and influencing plant growth. A bacterial isolate, Microbacterium testaceum Y411, was found to be the most active producer of indole-3-acetic acid (IAA). The maximum IAA production (170µg/mL) was recorded with the bacterium at optimum process parameters such as pH 7, temperature 30°C, and tryptophan 1000 µg/mL in a culture medium for 48 h. The extracted auxin was purified and analyzed by FT-IR, HPLC, and HR-MS, indicating bacterial auxin has a similar mass value to 4-chloroindole-3-acetic acid auxin. Furthermore, the bacterial auxin was tested on in vitro propagation of orchid, Cymbidium aloifolium, and 90% seed germination was recorded in Murashige and Skoog's medium supplemented with bacterial auxin. The novel results obtained in this study are used for agricultural applications and the Microbacterium testaceum Y411 is a valuable biotechnological resource for a natural auxin.
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Affiliation(s)
- Archana Yadav
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
- Department of Applied Biology, University of Science and Technology, Meghalaya, India
| | - Kalpataru Dutta Mudoi
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Niraj Kumar
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Sachin Rameshrao Geed
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Parishmita Gogoi
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Rabin K. Sharma
- Department of Applied Biology, University of Science and Technology, Meghalaya, India
| | - Ratul Saikia
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, Council of Scientific & Industrial Research (CSIR)-North East Institute of Science and Technology, Jorhat, Assam, India
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Jiang D, Liao L, Xing H, Chen Z, Luo X, Li HL. Interplay of Ecological Opportunities and Functional Traits Drives the Evolution and Diversification of Millettiod Legumes (Fabaceae). Genes (Basel) 2022; 13:genes13122220. [PMID: 36553487 PMCID: PMC9777679 DOI: 10.3390/genes13122220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the striking diversity of the angiosperms is a paramount issue in biology and of interest to biologists. The Millettiod legumes is one of the most hyper-diverse groups of the legume family, containing many economically important medicine, furniture and craft species. In the present study, we explore how the interplay of past climate change, ecological opportunities and functional traits' evolution may have triggered diversification of the Millettiod legumes. Using a comprehensive species-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that three dramatic accumulations of the Millettiod legumes occurred during the Miocene. The rapid diversification of the Millettiod legumes in the Miocene was driven by ecological opportunities created by the emergence of new niches and range expansion. Additionally, habit shifts and the switch between biomes might have facilitated the rapid diversification of the Millettiod legumes. The Millettiod legumes provide an excellent case for supporting the idea that the interplay of functional traits, biomes, and climatic and geographic factors drives evolutionary success.
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Kondo H, Deguchi A, Kikuchi S, Miyoshi K. Two pathways of 2n gamete formation and differences in the frequencies of 2n gametes between wild species and interspecific hybrids. PLANT CELL REPORTS 2022; 41:2187-2200. [PMID: 35984498 DOI: 10.1007/s00299-022-02915-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Epidendrum produces 2n gametes with high frequency. This paper is the first to report on multiple pathways for forming 2n gametes, meiotic defeats, and pre-meiotic chromosome doubling. Unreduced 2n reproductive cells are predominantly involved in pathways that lead to polyploid plants. Although one of the most common pathways for inducing 2n gametes is through meiotic defects, a small set of isolated species alternatively generates 2n gametes from tetraploid pollen mother cells in the pre-meiotic phase. Hence, determining the mechanisms underlying 2n gamete formation is critical to improving breeding programmes and understanding plant evolution. We investigated sporads to reveal the pathway(s) accounting for the formation and frequencies of 2n gametes in wild species and interspecific hybrids in the genus Epidendrum. We investigated different types of sporads with varying frequencies, sizes, and viability in the wild species and hybrids of the genus Epidendrum. Large tetrad-estimated pre-meiotic chromosome doubling was observed in wild species. The Epidendrum is unique in that it forms 2n pollens via two pathways, namely, meiotic defects and pre-meiotic chromosome doubling. These two pathways of 2n pollen formation could influence the high diversity generation of polyploidy with different degrees of heterozygosity and genetic backgrounds in the genus Epidendrum. Therefore, these findings are proposed to influence polyploid breeding of Epidendrum via 2n pollen, helping us understand evolution and speciation via unreduced 2n gamete formation in Orchidaceae.
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Affiliation(s)
- Haruka Kondo
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Ayumi Deguchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Kazumitsu Miyoshi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.
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Zhang M, Liu N, Teixeira da Silva JA, Liu X, Deng R, Yao Y, Duan J, He C. Physiological and transcriptomic analysis uncovers salinity stress mechanisms in a facultative crassulacean acid metabolism plant Dendrobium officinale. FRONTIERS IN PLANT SCIENCE 2022; 13:1028245. [PMID: 36275597 PMCID: PMC9582936 DOI: 10.3389/fpls.2022.1028245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Dendrobium officinale is a precious medicinal Chinese herb that employs facultative crassulacean acid metabolism (CAM) and has a high degree of abiotic stress tolerance, but the molecular mechanism underlying the response of this orchid to abiotic stresses is poorly understood. In this study, we analyzed the root microstructure of D. officinale plantlets and verified the presence of chloroplasts by transmission electron microscopy. To obtain a more comprehensive overview of the molecular mechanism underlying their tolerance to abiotic stress, we performed whole-transcriptome sequencing of the roots of 10-month-old plantlets exposed to salt (NaCl) treatment in a time-course experiment (0, 4 and 12 h). The total of 7376 differentially expressed genes that were identified were grouped into three clusters (P < 0.05). Metabolic pathway analysis revealed that the expression of genes related to hormone (such as auxins, cytokinins, abscisic acid, ethylene and jasmonic acid) biosynthesis and response, as well as the expression of genes related to photosynthesis, amino acid and flavonoid metabolism, and the SOS pathway, were either up- or down-regulated after salt treatment. Additionally, we identified an up-regulated WRKY transcription factor, DoWRKY69, whose ectopic expression in Arabidopsis promoted seed germination under salt tress. Collectively, our findings provide a greater understanding of the salt stress response mechanisms in the roots of a facultative CAM plant. A number of candidate genes that were discovered may help plants to cope with salt stress when introduced via genetic engineering.
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Affiliation(s)
- Mingze Zhang
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Nan Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Rufang Deng
- Opening Public Laboratory, Chinese Academy of Sciences, Guangzhou, China
| | - Yuxian Yao
- The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Wang J, Li J, Lin W, Deng B, Lin L, Lv X, Hu Q, Liu K, Fatima M, He B, Qiu D, Ma X. Genome-wide identification and adaptive evolution of CesA/Csl superfamily among species with different life forms in Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:994679. [PMID: 36247544 PMCID: PMC9559377 DOI: 10.3389/fpls.2022.994679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Orchidaceae, with more than 25,000 species, is one of the largest flowering plant families that can successfully colonize wide ecological niches, such as land, trees, or rocks, and its members are divided into epiphytic, terrestrial, and saprophytic types according to their life forms. Cellulose synthase (CesA) and cellulose synthase-like (Csl) genes are key regulators in the synthesis of plant cell wall polysaccharides, which play an important role in the adaptation of orchids to resist abiotic stresses, such as drought and cold. In this study, nine whole-genome sequenced orchid species with three types of life forms were selected; the CesA/Csl gene family was identified; the evolutionary roles and expression patterns of CesA/Csl genes adapted to different life forms and abiotic stresses were investigated. The CesA/Csl genes of nine orchid species were divided into eight subfamilies: CesA and CslA/B/C/D/E/G/H, among which the CslD subfamily had the highest number of genes, followed by CesA, whereas CslB subfamily had the least number of genes. Expansion of the CesA/Csl gene family in orchids mainly occurred in the CslD and CslF subfamilies. Conserved domain analysis revealed that eight subfamilies were conserved with variations in orchids. In total, 17 pairs of CesA/Csl homologous genes underwent positive selection, of which 86%, 14%, and none belonged to the epiphytic, terrestrial, and saprophytic orchids, respectively. The inter-species collinearity analysis showed that the CslD genes expanded in epiphytic orchids. Compared with terrestrial and saprophytic orchids, epiphytic orchids experienced greater strength of positive selection, with expansion events mostly related to the CslD subfamily, which might have resulted in strong adaptability to stress in epiphytes. Experiments on stem expression changes under abiotic stress showed that the CslA might be a key subfamily in response to drought stress for orchids with different life forms, whereas the CslD might be a key subfamily in epiphytic and saprophytic orchids to adapt to freezing stress. This study provides the basic knowledge for the further systematic study of the adaptive evolution of the CesA/Csl superfamily in angiosperms with different life forms, and research on orchid-specific functional genes related to life-history trait evolution.
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Affiliation(s)
- Jingjing Wang
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Li
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ban Deng
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lixian Lin
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanrui Lv
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kunpeng Liu
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mahpara Fatima
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bizhu He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongliang Qiu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, School of Future Technology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Wen Y, Qin Y, Shao B, Li J, Ma C, Liu Y, Yang B, Jin X. The extremely reduced, diverged and reconfigured plastomes of the largest mycoheterotrophic orchid lineage. BMC PLANT BIOLOGY 2022; 22:448. [PMID: 36123622 PMCID: PMC9487142 DOI: 10.1186/s12870-022-03836-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Plastomes of heterotrophic plants have been greatly altered in structure and gene content, owing to the relaxation of selection on photosynthesis-related genes. The orchid tribe Gastrodieae is the largest and probably the oldest mycoheterotrophic clade of the extant family Orchidaceae. To characterize plastome evolution across members of this key important mycoheterotrophic lineage, we sequenced and analyzed the plastomes of eleven Gastrodieae members, including representative species of two genera, as well as members of the sister group Nervilieae. RESULTS The plastomes of Gastrodieae members contain 20 protein-coding, four rRNA and five tRNA genes. Evolutionary analysis indicated that all rrn genes were transferred laterally and together, forming an rrn block in the plastomes of Gastrodieae. The plastome GC content of Gastrodia species ranged from 23.10% (G. flexistyla) to 25.79% (G. javanica). The plastome of Didymoplexis pallens contains two copies each of ycf1 and ycf2. The synonymous and nonsynonymous substitution rates were very high in the plastomes of Gastrodieae among mycoheterotrophic species in Orchidaceae and varied between genes. CONCLUSIONS The plastomes of Gastrodieae are greatly reduced and characterized by low GC content, rrn block formation, lineage-specific reconfiguration and gene content, which might be positively selected. Overall, the plastomes of Gastrodieae not only serve as an excellent model for illustrating the evolution of plastomes but also provide new insights into plastome evolution in parasitic plants.
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Affiliation(s)
- Yingying Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Ying Qin
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China
| | - Bingyi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, 666303, China
| | - Chongbo Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Liu
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China.
| | - Boyun Yang
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00575-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Jiang L, Lin M, Wang H, Song H, Zhang L, Huang Q, Chen R, Song C, Li G, Cao Y. Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1340-1353. [PMID: 35785503 DOI: 10.1111/tpj.15892] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.
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Affiliation(s)
- Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, 241000, China
| | - Mengfei Lin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330224, Jiangxi, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Song
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Zhang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Qingyu Huang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Renrui Chen
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Guohui Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
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48
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Jolman D, Batalla MI, Hungerford A, Norwood P, Tait N, Wallace LE. The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11496. [PMID: 36258786 PMCID: PMC9575117 DOI: 10.1002/aps3.11496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Lewis Knudson first successfully germinated orchid seeds asymbiotically on artificial medium in 1922. While many orchid species have since been grown asymbiotically, the tremendous variation in how species respond to artificial medium and growth conditions ex situ has also become apparent in the past century. In this study, we reviewed published journal articles on asymbiotic orchid seed germination to provide a summary of techniques used and to evaluate if these differ between terrestrial and epiphytic species, to identify areas where additional research is needed, and to evaluate whether asymbiotic germination could be used more often in ex situ conservation. We found articles reporting successful asymbiotic germination of 270 species and 20 cultivars across Orchidaceae. Researchers often used different techniques with epiphytic versus terrestrial species, but species-specific responses to growth media and conditions were common, indicating that individualized protocols will be necessary for most species. The widespread success in generating seedlings on artificial media suggests that asymbiotic techniques should be another tool for the conservation of rare orchid species. Further advances are needed in understanding how to introduce mycorrhizae to axenically grown orchids and to maximize the viability of seedlings reintroduced into natural habitats to fully utilize these methods for conservation.
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Affiliation(s)
- Devani Jolman
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
| | - Martín I. Batalla
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
| | - Alexis Hungerford
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
| | - Pryce Norwood
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
| | - Noah Tait
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
| | - Lisa E. Wallace
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
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Niche conservatism and evolution of climatic tolerance in the Neotropical orchid genera Sobralia and Brasolia (Orchidaceae). Sci Rep 2022; 12:13936. [PMID: 35978043 PMCID: PMC9385687 DOI: 10.1038/s41598-022-18218-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Sobralia and Brasolia form a large complex of Neotropical Orchidaceae. Although the molecular and morphological studies allowed to increase the rate of work on the modern classification of the taxa, they still require the attention as remaining without complete revision. The niche similarity analysis between representatives of Sobralia and recently segregated from this taxon—genus Brasolia is presented. The ecological tolerance evolution within the group was investigated with molecular clock analysis and phylogeny as the background. The phylogenetic analysis has confirmed the previous results and placed Brasolia representatives in a single clade with Elleanthus and Sobralia core as a separated group. The molecular clock analysis suggests that Sobralia and Brasolia are relatively young groups that evolved between 8.5 and 8 million years ago. Distribution of suitable niches of studied species is generally congruent with the known geographical ranges of particular taxa. The calculated niche overlap did not indicate any correlation between niche overlap and species phylogenetic relationships and remains low for both intra- and intergeneric relationships. The reconstruction of climatic tolerance evolution indicated that the studied species of Brasolia and Sobralia are characterized by generally similar ecological tolerance for most of the analyzed variables.
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Moraes AP, Engel TBJ, Forni-Martins ER, de Barros F, Felix LP, Cabral JS. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. ANNALS OF BOTANY 2022; 130:11-25. [PMID: 35143612 PMCID: PMC9295925 DOI: 10.1093/aob/mcac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework. METHODS Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample. KEY RESULTS The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments. CONCLUSIONS The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.
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Affiliation(s)
| | - Thaissa Brogliato Junqueira Engel
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Eliana R Forni-Martins
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado, São Paulo, 04045-972, São Paulo, Brazil
| | - Leonardo P Felix
- Universidade Federal da Paraíba – UFPB, Campus II, Departamento de Ciências Biológicas, Areia, 58397-000, Paraíba, Brazil
| | - Juliano Sarmento Cabral
- University of Würzburg, Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), Klara-Oppenheimer-Weg 32, D-97074, Würzburg, Germany
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