1
|
Li R, Gao X, Wu Y, Wei C, Li MH, Liu DK, Liu ZJ. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC. Int J Mol Sci 2024; 25:2055. [PMID: 38396732 PMCID: PMC10888551 DOI: 10.3390/ijms25042055] [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: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
Collapse
Affiliation(s)
- Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Yuwei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Chunyi Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, 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 Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
2
|
Wang X, Gao Y, Zang P, Zhang G, Yang X, Liu Q. Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation. FRONTIERS IN PLANT SCIENCE 2024; 15:1334958. [PMID: 38379940 PMCID: PMC10877603 DOI: 10.3389/fpls.2024.1334958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Introduction Asexual reproduction of Gastrodia elata Bl. f. glauca S. chow (GeB) produces degeneration with increasing number of GeB. Therefore, we analyzed the microorganisms of GeB seedlings and surrounding soil by Illumina Miseq high-throughput sequencing technology. Methods In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the types and quantities of GeB seedlings and surrounding soil microorganisms in the first to third generations of asexual reproduction, isolated and identified the dominant strains of GeB in the first to third generations and screened the antagonistic bacteria of its pathogenic fungi, and evaluated the effects of beneficial bacteria on the production performance of seedlings planted with GeB. Results With an increase in the number of asexual reproductive generations, the number of pathogenic fungi and bacteria in GeB seedlings and the surrounding soil increased, and the number of beneficial fungi and bacteria decreased. Pseudomonas sp., Agrobacterium rhizomes, and Herbaspirillum hiltneri were isolated and identified in the first generation, and Trichoderma harzianum, Penicillium viridiatum, Fusarium oxysporum, and Novosphingobium sp. Were isolated and identified in the third generation. Antagonistic strains of the three pathogenic bacterial strains were screened. In conclusion, beneficial bacteria significantly improved the production performance of asexual reproductive seedlings planted with GeB. Discussion In conclusion, our findings suggested that the microorganisms of GeB seedlings and the surrounding soil change as the number of generations of GeB reproduction increases, disrupts the microecological balance of surrounding soil and endophytic microbiomes.This study provides a theoretical basis for the degradation of asexual reproduction in GeB.
Collapse
Affiliation(s)
- Xi Wang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Yugang Gao
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Pu Zang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Ge Zhang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Xinyu Yang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Qun Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
3
|
Liu JJ, Yang XQ, Li ZY, Miao JY, Li SB, Zhang WP, Lin YC, Lin LB. The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): a comprehensive review. FRONTIERS IN PLANT SCIENCE 2024; 14:1309038. [PMID: 38264031 PMCID: PMC10804856 DOI: 10.3389/fpls.2023.1309038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Gastrodia elata Blume, a fully mycoheterotrophic perennial plant of the family Orchidaceae, is a traditional Chinese herb with medicinal and edible value. Interestingly, G. elata requires symbiotic relationships with Mycena and Armillaria strains for seed germination and plant growth, respectively. However, there is no comprehensive summary of the symbiotic mechanism between fungi and G. elata. Here, the colonization and digestion of hyphae, the bidirectional exchange of nutrients, the adaptation of fungi and G. elata to symbiosis, and the role of microorganisms and secondary metabolites in the symbiotic relationship between fungi and G. elata are summarized. We comprehensively and deeply analyzed the mechanism of symbiosis between G. elata and fungi from three perspectives: morphology, nutrition, and molecules. The aim of this review was to enrich the understanding of the mutualistic symbiosis mechanisms between plants and fungi and lay a theoretical foundation for the ecological cultivation of G. elata.
Collapse
Affiliation(s)
- Jia-Jia Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
- Yunnan Key Laboratory of Gastrodia and Fungal Symbiotic Biology, Zhaotong University, Zhaotong, Yunnan, China
| | - Xiao-Qi Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Zong-Yang Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Jia-Yun Miao
- Yunnan Senhao Fungi Industry Co., Ltd, Zhaotong, Yunnan, China
| | - Shi-Bo Li
- Yunnan Senhao Fungi Industry Co., Ltd, Zhaotong, Yunnan, China
| | - Wen-Ping Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yi-Cen Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
- Yunnan Key Laboratory of Gastrodia and Fungal Symbiotic Biology, Zhaotong University, Zhaotong, Yunnan, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| |
Collapse
|
4
|
Minasiewicz J, Zwolicki A, Figura T, Novotná A, Bocayuva MF, Jersáková J, Selosse MA. Stoichiometry of carbon, nitrogen and phosphorus is closely linked to trophic modes in orchids. BMC PLANT BIOLOGY 2023; 23:422. [PMID: 37700257 PMCID: PMC10496321 DOI: 10.1186/s12870-023-04436-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/04/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Mycorrhiza is a ubiquitous form of symbiosis based on the mutual, beneficial exchange of resources between roots of autotrophic (AT) plants and heterotrophic soil fungi throughout a complex network of fungal mycelium. Mycoheterotrophic (MH) and mixotrophic (MX) plants can parasitise this system, gaining all or some (respectively) required nutrients without known reciprocity to the fungus. We applied, for the first time, an ecological stoichiometry framework to test whether trophic mode of plants influences their elemental carbon (C), nitrogen (N), and phosphorus (P) composition and may provide clues about their biology and evolution within the framework of mycorrhizal network functioning. RESULTS We analysed C:N:P stoichiometry of 24 temperate orchid species and P concentration of 135 species from 45 plant families sampled throughout temperate and intertropical zones representing the three trophic modes (AT, MX and MH). Welch's one-way ANOVA and PERMANOVA were used to compare mean nutrient values and their proportions among trophic modes, phylogeny, and climate zones. Nutrient concentration and stoichiometry significantly differentiate trophic modes in orchids. Mean foliar C:N:P stoichiometry showed a gradual increase of N and P concentration and a decrease of C: nutrients ratio along the trophic gradient AT < MX < MH, with surprisingly high P requirements of MH orchids. Although P concentration in orchids showed the trophy-dependent pattern regardless of climatic zone, P concentration was not a universal indicator of trophic modes, as shown by ericaceous MH and MX plants. CONCLUSION The results imply that there are different evolutionary pathways of adaptation to mycoheterotrophic nutrient acquisition, and that the high nutrient requirements of MH orchids compared to MH plants from other families may represent a higher cost to the fungal partner and consequently lead to the high fungal specificity observed in MH orchids.
Collapse
Affiliation(s)
- Julita Minasiewicz
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland.
| | - Adrian Zwolicki
- Faculty of Biology, Department of Vertebrate Ecology and Zoology, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Tomáš Figura
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, Průhonice, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, 12844, Czech Republic
- Evolution, Biodiversité (ISYEB), Institut de Systématique, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, Paris, CP 39, F-75005, France
| | - Alžběta Novotná
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
- Institute of Microbiology ASCR, Vídeňská, Praha, 1083, 142 20, Czech Republic
| | - Melissa F Bocayuva
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street, Viçosa, Minas Gerais, CEP: 36570-900, Brazil
| | - Jana Jersáková
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, 1760, 37005, Czech Republic
| | - Marc-André Selosse
- Faculty of Biology, Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street, Viçosa, Minas Gerais, CEP: 36570-900, Brazil
- Evolution, Biodiversité (ISYEB), Institut de Systématique, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, Paris, CP 39, F-75005, France
| |
Collapse
|
5
|
Shao BY, Wang MZ, Chen SS, Ya JD, Jin XH. Habitat-related plastome evolution in the mycoheterotrophic Neottia listeroides complex (Orchidaceae, Neottieae). BMC PLANT BIOLOGY 2023; 23:282. [PMID: 37244988 DOI: 10.1186/s12870-023-04302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Mycoheterotrophs, acquiring organic carbon and other nutrients from mycorrhizal fungi, have evolved repeatedly with substantial plastid genome (plastome) variations. To date, the fine-scale evolution of mycoheterotrophic plastomes at the intraspecific level is not well-characterized. A few studies have revealed unexpected plastome divergence among species complex members, possibly driven by various biotic/abiotic factors. To illustrate evolutionary mechanisms underlying such divergence, we analyzed plastome features and molecular evolution of 15 plastomes of Neottia listeroides complex from different forest habitats. RESULTS These 15 samples of Neottia listeroides complex split into three clades according to their habitats approximately 6 million years ago: Pine Clade, including ten samples from pine-broadleaf mixed forests, Fir Clade, including four samples from alpine fir forests and Fir-willow Clade with one sample. Compared with those of Pine Clade members, plastomes of Fir Clade members show smaller size and higher substitution rates. Plastome size, substitution rates, loss and retention of plastid-encoded genes are clade-specific. We propose to recognized six species in N. listeroides complex and slightly modify the path of plastome degradation. CONCLUSIONS Our results provide insight into the evolutionary dynamics and discrepancy of closely related mycoheterotrophic orchid lineages at a high phylogenetic resolution.
Collapse
Affiliation(s)
- Bing-Yi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mo-Zhu Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Si-Si Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
6
|
Chen ZH, Zhang ZY, Song XQ, Zhang Z. Gastrodiabawanglingensis (Orchidaceae, Epidendroideae), a new species from Hainan Island, China. PHYTOKEYS 2023; 220:39-50. [PMID: 37251611 PMCID: PMC10209714 DOI: 10.3897/phytokeys.220.95137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/31/2023] [Indexed: 05/31/2023]
Abstract
Gastrodiabawanglingensis, a new species of Orchidaceae from Hainan Island, China, is described and illustrated. It is morphologically similar to G.theana, G.albidoides and G.albida with dwarf habits, scarcely opening flowers, elongated fruit stems, curved and fleshy perianth tubes and similar columns and lips, but can be easily distinguished from them by having a pair of lateral wings bent outwards at the apex of the column and lateral wings with acuminate tips lower than the anther. According to the IUCN Red List Categories and Criteria, the new species is assessed as Endangered (EN). The plastome of G.bawanglingensis is greatly reduced and reconfigured with approximately 30876 bp in size and 25.36% in GC content. Morphological characteristics and molecular phylogenetic results based on chloroplast gene sequences support the recognition of G.bawanglingensis as a new species within Gastrodia.
Collapse
Affiliation(s)
- Zhi-Heng Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou 570228, China
| | - Zhong-Yang Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xi-Qiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou 570228, China
- College of Forestry, Hainan University, Haikou 570228, China
| | - Zhe Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou 570228, China
- College of Forestry, Hainan University, Haikou 570228, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Song C, Wang Y, Manzoor MA, Mao D, Wei P, Cao Y, Zhu F. In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1018029. [PMID: 36212315 PMCID: PMC9539832 DOI: 10.3389/fpls.2022.1018029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.
Collapse
Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yan Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Di Mao
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yunpeng Cao
- Chinese Academy of Sciences (CAS) Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| |
Collapse
|