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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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Kim H, Choi B, Lee C, Paik JH, Jang CG, Weiss-Schneeweiss H, Jang TS. Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)? BMC PLANT BIOLOGY 2023; 23:485. [PMID: 37817118 PMCID: PMC10565974 DOI: 10.1186/s12870-023-04456-9] [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: 05/10/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation. RESULTS The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels. CONCLUSIONS This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.
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Affiliation(s)
- Hyeonjin Kim
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Bokyung Choi
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Changyoung Lee
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jin-Hyub Paik
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Chang-Gee Jang
- Department of Biology Education, Kongju National University, Gongju, 32588, Republic of Korea
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, A-1030, Austria.
| | - Tae-Soo Jang
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
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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: 0] [Impact Index Per Article: 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.
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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
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Bai MZ, Guo YY. Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing. Int J Mol Sci 2023; 24:13620. [PMID: 37686425 PMCID: PMC10487979 DOI: 10.3390/ijms241713620] [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: 07/23/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants.
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Affiliation(s)
| | - Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
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Meng Y, Liang Z, Zhang L, Hu L, Fu J, Wei G, Huang Y. Identification of three types of O-glycosylated flavonoids in Dendrobium loddigesii, Dendrobium primulinum, Dendrobium crepidatum, Dendrobium porphyrochilum, and Dendrobium hancockii using mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9421. [PMID: 36279199 DOI: 10.1002/rcm.9421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
RATIONALE Flavonoids, representing the pharmacologically active ingredients, are found widely in Dendrobium species. The biodiversity of Dendrobium makes the identification of its varieties all the more complicated. Previous studies showed that C-glycosylated flavones and a few O-glycosylated flavonols could be used in the identification of various Dendrobium species. Accordingly, this study further explores the significance of the identification of various types of O-glycosylated flavonoids in Dendrobium species. METHODS High-performance liquid chromatography coupled with electrospray ionization multistage tandem mass spectrometry (HPLC-ESI-MSn ) was used to identify the chemical constituents in five types of Dendrobium: Dendrobium loddigesii, Dendrobium primulinum, Dendrobium crepidatum, Dendrobium porphyrochilum, and Dendrobium hancockii. RESULTS A total of 41 O-glycosylated flavonoids and 3 C-glycosylated flavones were identified, among which O-glycosylated dihydroflavones were the main flavonoids in D. loddigesii and D. primulinum, O-Glycosylated flavonols were rich in both D. crepidatum and D. porphyrochilum characterized by the main aglycone, substituted sugars, and their structural characteristics, and O-glycosylated flavones were the main constituents in D. hancockii. CONCLUSIONS In this study, three types of O-glycosylated flavonoids in the five Dendrobium species were determined to have certain significance. This also provides a reference for the identification of other O-glycosylated flavonoids in Chinese herbs.
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Affiliation(s)
- Yuanjun Meng
- The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhiyun Liang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lin Zhang
- The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Hu
- The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingran Fu
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gang Wei
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
- Shaoguan Institute of Danxia Dendrobium Officinale (SIDDO), Shaoguan, China
| | - Yuechun Huang
- The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
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Wang Y, Chen Y, Wei Q, Chen X, Wan H, Sun C. Characterization of repetitive sequences in Dendrobium officinale and comparative chromosomal structures in Dendrobium species using FISH. Gene 2022; 846:146869. [PMID: 36075328 DOI: 10.1016/j.gene.2022.146869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Tandem repeats are one of the most conserved features in the eukaryote genomes. Dendrobium is the third largest genus in family Orchidaceae compromising over 1,200 species. However, the organization of repetitive sequences in Dendrobium species remains unclear. In this study, we performed the identification and characterization of the tandem repeats in D. officinale genome using graph-based clustering and Fluorescence in situ hybridization (FISH). Six major clusters including five satellite DNAs (DofSat1-5) and one 5S rDNA repeat (Dof5S) were identified as tandem repeats. The tandem organization of DofSat5 was verified by PCR amplification and southern blotting. The chromosomal locations of the repetitive DNAs in D. officinale were investigated by FISH using the tandem repeats and oligos probes. The results showed that each of the DofSat5, 5S and 45S rDNA had one pair of strong signals on D. officinale chromosomes. The distribution of repetitive DNAs along chromosomes was also investigated based on genomic in situ hybridization (GISH) among four Dendrobium species. The results suggested complex chromosomal fusion/segmentation and rearrangements during the evolution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differentiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.
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Affiliation(s)
- Yunzhu Wang
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yue Chen
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyang Chen
- Seed Management Terminal of Zhejiang, Hangzhou 310021, China.
| | - Hongjian Wan
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Chongbo Sun
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, 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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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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Baranow P, Rojek J, Dudek M, Szlachetko D, Bohdanowicz J, Kapusta M, Jedrzejczyk I, Rewers M, Moraes AP. Chromosome Number and Genome Size Evolution in Brasolia and Sobralia (Sobralieae, Orchidaceae). Int J Mol Sci 2022; 23:ijms23073948. [PMID: 35409308 PMCID: PMC8999598 DOI: 10.3390/ijms23073948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the clear circumscription of tribe Sobralieae (Orchidaceae), its internal relationships are still dubious. The recently delimited genus Brasolia, based on previous Sobralia species, is now assumed to be paraphyletic, with a third genus, Elleanthus, nested in it. The morphology of these three genera is significantly different, indicating the necessity of new data for a better genera delimitation. Though morphology and molecular data are available, cytogenetics data for Sobralieae is restricted to two Sobralia and one Elleanthus species. Aiming to evaluate the potential of cytogenetic data for Brasolia-Elleanthus-Sobralia genera delimitation, we present chromosome number and genome size data for 21 and 20 species, respectively, and used such data to infer the pattern of karyotype evolution in these genera. The analysis allowed us to infer x = 24 as the base chromosome number and genome size of average 1C-value of 5.0 pg for the common ancestor of Brasolia-Elleanthus-Sobralia. The recurrent descending dysploidy in Sobralieae and the punctual genome upsize suggest a recent diversification in Sobralieae but did not allow differing between Brasolia and Sobralia. However, the basal position of tribe Sobralieae in the subfamily Epidendroideae makes this tribe of interest to further studies clarifying the internal delimitation and pattern of karyotype evolution.
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Affiliation(s)
- Przemysław Baranow
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
- Correspondence:
| | - Magdalena Dudek
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Dariusz Szlachetko
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Jerzy Bohdanowicz
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
| | - Iwona Jedrzejczyk
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave 7, 85-796 Bydgoszcz, Poland; (I.J.); (M.R.)
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave 7, 85-796 Bydgoszcz, Poland; (I.J.); (M.R.)
| | - Ana Paula Moraes
- Laboratory of Cytogenomic and Evolution of Plants, Center of Natural and Human Science, Federal University of ABC (UFABC), Sao Bernardo do Campo 09606-045, SP, Brazil;
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10
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Wei YL, Jin JP, Liang D, Gao J, Li J, Xie Q, Lu CQ, Yang FX, Zhu GF. Genome-wide identification of Cymbidium sinense WRKY gene family and the importance of its Group III members in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:969010. [PMID: 35968117 PMCID: PMC9365948 DOI: 10.3389/fpls.2022.969010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 05/13/2023]
Abstract
Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.
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Li J, Wu K, Li L, Wang M, Fang L, Zeng S. Cytological, Biochemical, and Transcriptomic Analyses of a Novel Yellow Leaf Variation in a Paphiopedilum (Orchidaceae) SCBG COP15. Genes (Basel) 2021; 13:71. [PMID: 35052412 PMCID: PMC8775194 DOI: 10.3390/genes13010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Paphiopedilum, belonging to the Orchidaceae, has high ornamental value. Leaf variations can considerably improve the economic and horticultural value of the orchids. In the study, a yellow leaf mutant of a Paphiopedilum hybrid named P. SCBG COP15 was identified during the in vitro plant culture process; however, little is known about their molecular mechanisms. For this, RNA-seq libraries were created and used for the transcriptomic profiling of P. SCBG COP15 and the yellow mutant. The Chl a, Chl b, and carotenoid contents in the yellow leaves decreased by approximately 75.99%, 76.92%, and 56.83%, respectively, relative to the green leaves. Decreased chloroplasts per cell and abnormal chloroplast ultrastructure were observed by electron microscopic investigation in yellowing leaves; photosynthetic characteristics and Chl fluorescence parameters were also decreased in the mutant. Altogether, 34,492 unigenes were annotated by BLASTX; 1,835 DEGs were identified, consisting of 697 upregulated and 1138 downregulated DEGs. HEMA, CRD, CAO, and CHLE, involved in Chl biosynthesis, were predicted to be key genes responsible for leaf yellow coloration. Our findings provide an essential genetic resource for understanding the molecular mechanism of leaf color variation and breeding new varieties of Paphiopedilum with increased horticultural value.
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Affiliation(s)
- Ji Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (J.L.); (K.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (J.L.); (K.W.); (L.L.)
| | - Lin Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (J.L.); (K.W.); (L.L.)
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization/National Orchid Conservation Center of China/Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China;
| | - Lin Fang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (J.L.); (K.W.); (L.L.)
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (J.L.); (K.W.); (L.L.)
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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12
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Zhang FP, Zhang SB. Genome Size and Labellum Epidermal Cell Size Are Evolutionarily Correlated With Floral Longevity in Paphiopedilum Species. FRONTIERS IN PLANT SCIENCE 2021; 12:793516. [PMID: 34975981 PMCID: PMC8716874 DOI: 10.3389/fpls.2021.793516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/19/2021] [Indexed: 06/02/2023]
Abstract
Genome size is known to influence phenotypic traits in leaves and seeds. Although genome size is closely related to cellular and developmental traits across biological kingdoms, floral longevity is a floral trait with important fitness consequence, but less is known about the link between floral longevity and sizes of genomes and cells. In this study, we examined evolutionary coordination between genome size, floral longevity, and epidermal cell size in flowers and leaves in 13 Paphiopedilum species. We found that, across all the study species, the genome size was positively correlated with floral longevity but negatively associated with labellum epidermal cell size, and a negative relationship was found between floral longevity and labellum epidermal cell size. This suggested that genome size is potentially correlated with floral longevity, and genome size has an important impact on life-history trait. In addition, genome size was positively correlated with leaf epidermal cell size, which was different from the relationship in flower due to different selective pressures they experienced or different functions they performed. Therefore, genome size constraints floral longevity, and it is a strong predictor of cell size. The impact of genome size on reproduction might have more implications for the evolution of flowering plants and pollination ecology.
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Affiliation(s)
- Feng-Ping Zhang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Shi-Bao Zhang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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13
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Zhang ZS, Zeng QY, Liu YJ. Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L. BMC PLANT BIOLOGY 2021; 21:535. [PMID: 34773988 PMCID: PMC8590345 DOI: 10.1186/s12870-021-03313-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUNDS Populus and Salix belong to Salicaceae and are used as models to investigate woody plant physiology. The variation of karyotype and nuclear DNA content can partly reflect the evolutionary history of the whole genome, and can provide critical information for understanding, predicting, and potentially ameliorating the woody plant traits. Therefore, it is essential to study the chromosome number (CN) and genome size in detail to provide information for revealing the evolutionary process of Salicaceae. RESULTS In this study, we report the somatic CNs of seventeen species from eight genera in Salicaceae. Of these, CNs for twelve species and for five genera are reported for the first time. Among the three subfamilies of Salicaceae, the available data indicate CN in Samydoideae is n = 21, 22, 42. The only two genera, Dianyuea and Scyphostegia, in Scyphostegioideae respectively have n = 9 and 18. In Salicoideae, Populus, Salix and five genera closely related to them (Bennettiodendron, Idesia, Carrierea, Poliothyrsis, Itoa) are based on relatively high CNs from n = 19, 20, 21, 22 to n = 95 in Salix. However, the other genera of Salicoideae are mainly based on relatively low CNs of n = 9, 10, 11. The genome sizes of 35 taxa belonging to 14 genera of Salicaceae were estimated. Of these, the genome sizes of 12 genera and all taxa except Populus euphratica are first reported. Except for Dianyuea, Idesia and Bennettiodendron, all examined species have relatively small genome sizes of less than 1 pg, although polyploidization exists. CONCLUSIONS The variation of CN and genome size across Salicaceae indicates frequent ploidy changes and a widespread sharing of the salicoid whole genome duplication (WGD) by the relatives of Populus and Salix. The shrinkage of genome size after WGD indicates massive loss of genomic components. The phylogenetic asymmetry in clade of Populus, Salix, and their close relatives suggests that there is a lag-time for the subsequent radiations after the salicoid WGD event. Our results provide useful data for studying the evolutionary events of Salicaceae.
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Affiliation(s)
- Zhong-Shuai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China.
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14
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Chung O, Kim J, Bolser D, Kim HM, Jun JH, Choi JP, Jang HD, Cho YS, Bhak J, Kwak M. A chromosome-scale genome assembly and annotation of the spring orchid (Cymbidium goeringii). Mol Ecol Resour 2021; 22:1168-1177. [PMID: 34687590 DOI: 10.1111/1755-0998.13537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022]
Abstract
Cymbidium goeringii, commonly known as the spring orchid, has long been favoured for horticultural purposes in Asian countries. It is a popular orchid with much demand for improvement and development for its valuable varieties. Until now, its reference genome has not been published despite its popularity and conservation efforts. Here, we report the de novo assembly of the C. goeringii genome, which is the largest among the orchids published to date, using a strategy that combines short- and long-read sequencing and chromosome conformation capture (Hi-C) information. The total length of all scaffolds is 3.99 Gb, with an N50 scaffold size of 178.2 Mb. A total of 29,556 protein-coding genes were annotated and 3.55 Gb (88.87% of genome) repetitive sequences were identified. We constructed pseudomolecular chromosomes using Hi-C, incorporating 89.4% of the scaffolds in 20 chromosomes. We identified 220 expanded and 106 contracted genes families in C. goeringii after divergence from its close relative. We also identified new gene families, resistance gene analogues and changes within the MADS-box genes, which control a diverse set of developmental processes during orchid evolution. Our high quality chromosomal-level assembly of C. goeringii can provide a platform for elucidating the genomic evolution of orchids, mining functional genes for agronomic traits and for developing molecular markers for accelerated breeding as well as accelerating conservation efforts.
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Affiliation(s)
- Oksung Chung
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, Korea
| | - Dan Bolser
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Geromics Ltd., Cambridge, UK
| | - Hak-Min Kim
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Je Hoon Jun
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jae-Pil Choi
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, Korea
| | - Hyun-Do Jang
- National Institute of Biological Resources, Environmental Research Complex, Incheon, Korea
| | - Yun Sung Cho
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jong Bhak
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Geromics Ltd., Cambridge, UK.,Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Myounghai Kwak
- National Institute of Biological Resources, Environmental Research Complex, Incheon, Korea
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15
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Zhang Y, Zhang GQ, Zhang D, Liu XD, Xu XY, Sun WH, Yu X, Zhu X, Wang ZW, Zhao X, Zhong WY, Chen H, Yin WL, Huang T, Niu SC, Liu ZJ. Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. HORTICULTURE RESEARCH 2021; 8:183. [PMID: 34465765 PMCID: PMC8408244 DOI: 10.1038/s41438-021-00621-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/01/2021] [Indexed: 05/03/2023]
Abstract
As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.
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Affiliation(s)
- Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China
| | - Guo-Qiang Zhang
- Laboratory for Orchid Conservation and Utilization, Orchid Conservation and Research Center, The National Orchid Conservation Center, Shenzhen, 518114, China
- School of Food Science and Technology, Foshan University, Foshan, 528225, China
| | - 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-Die 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
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin-Yu Xu
- 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
| | - Wei-Hong Sun
- 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
| | - Xia Yu
- 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
| | - Xiaoen Zhu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China
| | | | | | | | - Hongfeng Chen
- Key Laboratory of Plant Resources Conservation Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Wei-Lun Yin
- 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 Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China.
| | - Shan-Ce Niu
- College of Horticulture, Hebei Agricultural University, Baoding, 071000, 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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16
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Genome Size Diversity in Rare, Endangered, and Protected Orchids in Poland. Genes (Basel) 2021; 12:genes12040563. [PMID: 33924526 PMCID: PMC8070121 DOI: 10.3390/genes12040563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 01/25/2023] Open
Abstract
Orchidaceae is one of the largest and the most widespread plant families with many species threatened with extinction. However, only about 1.5% of orchids’ genome sizes have been known so far. The aim of this study was to estimate the genome size of 15 species and one infraspecific taxon of endangered and protected orchids growing wild in Poland to assess their variability and develop additional criterion useful in orchid species identification and characterization. Flow cytometric genome size estimation revealed that investigated orchid species possessed intermediate, large, and very large genomes. The smallest 2C DNA content possessed Liparis loeselii (14.15 pg), while the largest Cypripedium calceolus (82.10 pg). It was confirmed that the genome size is characteristic to the subfamily. Additionally, for four species Epipactis albensis, Ophrys insectifera, Orchis mascula, Orchis militaris and one infraspecific taxon, Epipactis purpurata f. chlorophylla the 2C DNA content has been estimated for the first time. Genome size estimation by flow cytometry proved to be a useful auxiliary method for quick orchid species identification and characterization.
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17
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Farminhão JNM, Verlynde S, Kaymak E, Droissart V, Simo-Droissart M, Collobert G, Martos F, Stévart T. Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability. Mol Phylogenet Evol 2021; 159:107105. [PMID: 33601026 DOI: 10.1016/j.ympev.2021.107105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17-18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.
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Affiliation(s)
- João N M Farminhão
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Plant Ecology and Biogeochemistry, C.P. 244, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe, 1050, Brussels, Belgium.
| | - Simon Verlynde
- Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY 10458-5126, USA; PhD Program in Biology, Graduate Center, City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Esra Kaymak
- Evolutionary Biology and Ecology, Faculté des Sciences, C.P. 160/12, Université Libre de Bruxelles, 50 Avenue F. Roosevelt, BE-1050 Brussels, Belgium
| | - Vincent Droissart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; AMAP Lab, Univ Montpellier, IRD, CNRS, INRAE, CIRAD, Montpellier, France; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Géromine Collobert
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Florent Martos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Tariq Stévart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Meise Botanic Garden, Domein van Bouchout, Nieuwelaan 38, B-1860 Meise, Belgium
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Gargiulo R, Kull T, Fay MF. Effective double-digest RAD sequencing and genotyping despite large genome size. Mol Ecol Resour 2021; 21:1037-1055. [PMID: 33351289 DOI: 10.1111/1755-0998.13314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double-digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set-specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.
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Affiliation(s)
| | - Tiiu Kull
- Estonian University of Life Sciences, Tartu, Estonia
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
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Guo YY, Yang JX, Li HK, Zhao HS. Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences. FRONTIERS IN PLANT SCIENCE 2021; 12:609729. [PMID: 33633763 PMCID: PMC7900419 DOI: 10.3389/fpls.2021.609729] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/20/2021] [Indexed: 05/07/2023]
Abstract
The size of the chloroplast genome (plastome) of autotrophic angiosperms is generally conserved. However, the chloroplast genomes of some lineages are greatly expanded, which may render assembling these genomes from short read sequencing data more challenging. Here, we present the sequencing, assembly, and annotation of the chloroplast genomes of Cypripedium tibeticum and Cypripedium subtropicum. We de novo assembled the chloroplast genomes of the two species with a combination of short-read Illumina data and long-read PacBio data. The plastomes of the two species are characterized by expanded genome size, proliferated AT-rich repeat sequences, low GC content and gene density, as well as low substitution rates of the coding genes. The plastomes of C. tibeticum (197,815 bp) and C. subtropicum (212,668 bp) are substantially larger than those of the three species sequenced in previous studies. The plastome of C. subtropicum is the longest one of Orchidaceae to date. Despite the increase in genome size, the gene order and gene number of the plastomes are conserved, with the exception of an ∼75 kb large inversion in the large single copy (LSC) region shared by the two species. The most striking is the record-setting low GC content in C. subtropicum (28.2%). Moreover, the plastome expansion of the two species is strongly correlated with the proliferation of AT-biased non-coding regions: the non-coding content of C. subtropicum is in excess of 57%. The genus provides a typical example of plastome expansion induced by the expansion of non-coding regions. Considering the pros and cons of different sequencing technologies, we recommend hybrid assembly based on long and short reads applied to the sequencing of plastomes with AT-biased base composition.
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The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants. Methods Mol Biol 2021; 2222:325-361. [PMID: 33301101 DOI: 10.1007/978-1-0716-0997-2_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the years, the amount of DNA in a nucleus (genome size) has been estimated using a variety of methods, but increasingly, flow cytometry (FCM) has become the method of choice. The popularity of this technique lies in the ease of sample preparation and in the large number of particles (i.e., nuclei) that can be analyzed in a very short period of time. This chapter presents a step-by-step guide to estimating the nuclear DNA content of plant nuclei using FCM. Attempting to serve as a tool for daily laboratory practice, we list, in detail, the equipment required, specific reagents and buffers needed, as well as the most frequently used protocols to carry out nuclei isolation. In addition, solutions to the most common problems that users may encounter when working with plant material and troubleshooting advice are provided. Finally, information about the correct terminology to use and the importance of obtaining chromosome counts to avoid cytological misinterpretations of the FCM data are discussed.
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21
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Morphological and Genetic Diversities of Habenaria radiata (Orchidaceae) in the Kinki Area, Japan. Int J Mol Sci 2020; 22:ijms22010311. [PMID: 33396777 PMCID: PMC7795838 DOI: 10.3390/ijms22010311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 11/16/2022] Open
Abstract
Floral organs have evolved from leaves for reproduction, and the morphological analyses help to understand the plant diversity and evolution. Habenaria radiata (syn. Pecteilis radiata) is a terrestrial orchid living in wetlands in Japan, Russia, South Korea, and China. The habitats of this plant in Japan have been reduced because of environmental destruction and overexploitation, and thus it is on the Red List of Japan as a Near Threatened species. One of the three petals of the H. radiata flower is called a lip or labellum, which resembles a flying white bird, egret, or white heron, with its proposed function being to attract pollinators. To understand the diversity of H. radiata plants in different areas, we examined the lip morphology and phylogeny of populations from eight habitats in the Kinki area, Japan. The complex shapes of the lips were quantified and presented as a radar chart, enabling characterization of the morphological difference among populations. Phylogenetic analysis with microsatellite markers that we generated showed the variation of genetic diversity among populations, suggesting the different degrees of inbreeding, outbreeding, and vegetative propagation. Our approach offers a basic method to characterize the morphological and genetic diversity in natural populations.
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22
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Baguette M, Bertrand JAM, Stevens VM, Schatz B. Why are there so many bee-orchid species? Adaptive radiation by intra-specific competition for mnesic pollinators. Biol Rev Camb Philos Soc 2020; 95:1630-1663. [PMID: 32954662 DOI: 10.1111/brv.12633] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 01/08/2023]
Abstract
Adaptive radiations occur mostly in response to environmental variation through the evolution of key innovations that allow emerging species to occupy new ecological niches. Such biological innovations may play a major role in niche divergence when emerging species are engaged in reciprocal ecological interactions. To demonstrate coevolution is a difficult task; only a few studies have confirmed coevolution as driver of speciation and diversification. Herein we review current knowledge about bee orchid (Ophrys spp.) reproductive biology. We propose that the adaptive radiation of the Mediterranean orchid genus Ophrys, comprising several hundred species, is due to coevolutionary dynamics between these plants and their pollinators. We suggest that pollination by sexual swindling used by Ophrys orchids is the main driver of this coevolution. Flowers of each Ophrys species mimic a sexually receptive female of one particular insect species, mainly bees. Male bees are first attracted by pseudo-pheromones emitted by Ophrys flowers that are similar to the sexual pheromones of their females. Males then are lured by the flower shape, colour and hairiness, and attempt to copulate with the flower, which glues pollen onto their bodies. Pollen is later transferred to the stigma of another flower of the same Ophrys species during similar copulation attempts. In contrast to rewarding pollination strategies, Ophrys pollinators appear to be parasitized. Here we propose that this apparent parasitism is in fact a coevolutionary relationship between Ophrys and their pollinators. For plants, pollination by sexual swindling could ensure pollination efficiency and specificity, and gene flow among populations. For pollinators, pollination by sexual swindling could allow habitat matching and inbreeding avoidance. Pollinators might use the pseudo-pheromones emitted by Ophrys to locate suitable habitats from a distance within complex landscapes. In small populations, male pollinators would disperse once they have memorized the local diversity of sexual pseudo-pheromone bouquets or if all Ophrys flowers are fertilized and thus repel pollinators via production of repulsive pheromones that mimic those produced by fertilized female bees. We propose the following evolutionary scenario: Ophrys radiation is driven by strong intra-specific competition among Ophrys individuals for the attraction of species-specific pollinators, which is a consequence of the high cognitive abilities of pollinators. Male bees record the pheromone signatures of kin or of previously courted partners to avoid further copulation attempts, thereby inducing strong selection on Ophrys for variation in odour bouquets emitted by individual flowers. The resulting odour bouquets could by chance correspond to pseudo-pheromones of the females of another bee species, and thus attract a new pollinator. If such pollinator shifts occur simultaneously in several indivuals, pollen exchanges might occur and initiate speciation. To reinforce the attraction of the new pollinator and secure prezygotic isolation, the following step is directional selection on flower phenotypes (shape, colour and hairiness) towards a better match with the body of the pollinator's female. Pollinator shift and the resulting prezygotic isolation is adaptive for new Ophrys species because they may benefit from competitor-free space for limited pollinators. We end our review by proritizing several critical research avenues.
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Affiliation(s)
- Michel Baguette
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, F-75005, Paris, France.,Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, F-09200, Moulis, France
| | - Joris A M Bertrand
- LGDP (Laboratoire Génome et Développement des Plantes) UMR5096, Université de Perpignan Via Domitia -CNRS, F-66860, Perpignan, France
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, F-09200, Moulis, France
| | - Bertrand Schatz
- CEFE (Centre d'Ecologie Fonctionnelle et Evolutive) UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry - EPHE, 1919 Route de Mende, 34293, Montpellier, France
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23
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Boutanaev AM, Nemchinov LG. Genome Size Dynamics within Multiple Genera of Diploid Seed Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Nguyen NH, Vu HT, Le ND, Nguyen TD, Duong HX, Tran HD. Molecular Identification and Evaluation of the Genetic Diversity of Dendrobium Species Collected in Southern Vietnam. BIOLOGY 2020; 9:E76. [PMID: 32290139 PMCID: PMC7236015 DOI: 10.3390/biology9040076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 01/12/2023]
Abstract
Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam.
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Affiliation(s)
- Nhu-Hoa Nguyen
- Faculty of Biology, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, Ward 4, District 5, Ho Chi Minh 72711, Vietnam
| | - Huyen-Trang Vu
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Ngoc-Diep Le
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Thanh-Diem Nguyen
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Hoa-Xo Duong
- Biotechnology Center of Ho Chi Minh City, 2374 Highway 1, Quarter 2, Ward Trung My Tay, District 12, Ho Chi Minh 71507, Vietnam;
| | - Hoang-Dung Tran
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
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25
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Ramya M, Jang S, An HR, Lee SY, Park PM, Park PH. Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation. Int J Mol Sci 2020; 21:ijms21031160. [PMID: 32050562 PMCID: PMC7037033 DOI: 10.3390/ijms21031160] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea;
| | - Hye-Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Su-Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pil-Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul 08826, Korea
- Correspondence: or ; Tel.: +82-10-4507-8321 or +82-63-238-6842; Fax: +82-63-238-6805
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26
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Kim SH, Kim SW, Lim GH, Lyu JI, Choi HI, Jo YD, Kang SY, Kang BC, Kim JB. Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation. PLoS One 2020; 15:e0228078. [PMID: 31995594 PMCID: PMC6988911 DOI: 10.1371/journal.pone.0228078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 11/23/2022] Open
Abstract
Leaf color is an important agronomic trait in flowering plants, including orchids. However, factors underlying leaf phenotypes in plants remain largely unclear. A mutant displaying yellow leaves was obtained by the γ-ray-based mutagenesis of a Cymbidium orchid and characterized using RNA sequencing. A total of 144,918 unigenes obtained from over 25 million reads were assigned to 22 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, gene ontology was used to classify the predicted functions of transcripts into 73 functional groups. The RNA sequencing analysis identified 2,267 differentially expressed genes between wild-type and mutant Cymbidium sp. Genes involved in the chlorophyll biosynthesis and degradation, as well as ion transport, were identified and assayed for their expression levels in wild-type and mutant plants using quantitative real-time profiling. No critical expression changes were detected in genes involved in chlorophyll biosynthesis. In contrast, seven genes involved in ion transport, including two metal ion transporters, were down-regulated, and chlorophyllase 2, associated with chlorophyll degradation, was up-regulated. Together, these results suggest that alterations in chlorophyll metabolism and/or ion transport might contribute to leaf color in Cymbidium orchids.
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Se Won Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Gah-Hyun Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
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Kim SH, Jo YD, Ryu J, Hong MJ, Kang BC, Kim JB. Effects of the total dose and duration of γ-irradiation on the growth responses and induced SNPs of a Cymbidium hybrid. Int J Radiat Biol 2019; 96:545-551. [PMID: 31852368 DOI: 10.1080/09553002.2020.1704303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose: Ionizing radiation has been used for developing new cultivars of diverse plant species, including Cymbidium orchid species. The effects of the total dose on mutation induction have been investigated; however, there is relatively little research on the influence of the dose rate or irradiation duration.Materials and methods: Thus, we analyzed the effects of the total dose and irradiation duration on the growth of Cymbidium hybrid RB001 protocorm-like bodies (PLBs). We completed a genotyping-by-sequencing analysis to compare the induced SNPs among five γ-irradiated populations with similar growth responses (LD50) to γ-rays.Results: The optimal time to assess the effects of the γ-irradiation was at 6 months after the treatment. On the basis of the survival rate of γ-irradiated PLBs, the optimal doses (LD50) for each irradiation duration were estimated: 1 h, 16.1 Gy; 4 h, 23.6 Gy; 8 h, 37.9 Gy; 16 h, 37.9 Gy; and 24 h, 40.0 Gy. The estimated optimal doses were duration-dependent at irradiation durations shorter than 8 h, but not at irradiation durations exceeding 8 h. A SNP comparison revealed a lack of significant differences among the mutations induced by γ-irradiations.Conclusions: These results indicate the irradiation duration affects PLB growth in response to γ-rays. Moreover, the mutations induced by a short-term treatment may be similar to those induced by a treatment over a longer period.
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
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Trávníček P, Čertner M, Ponert J, Chumová Z, Jersáková J, Suda J. Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions. THE NEW PHYTOLOGIST 2019; 224:1642-1656. [PMID: 31215648 DOI: 10.1111/nph.15996] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family. Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential. Pronounced variation in genome size (341-54 878 Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models. Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE.
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Affiliation(s)
- Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jan Ponert
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jana Jersáková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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29
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Sramkó G, Paun O, Brandrud MK, Laczkó L, Molnár A, Bateman RM. Iterative allogamy-autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae). ANNALS OF BOTANY 2019; 124:481-497. [PMID: 31231754 PMCID: PMC6798847 DOI: 10.1093/aob/mcz103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/19/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing. METHODS We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample. KEY RESULTS The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine, is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams. CONCLUSIONS This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine, which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams.
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Affiliation(s)
- Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Debrecen, Hungary
- For correspondence. E-mail
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Levente Laczkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Attila Molnár
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
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Ramya M, Park PH, Chuang YC, Kwon OK, An HR, Park PM, Baek YS, Kang BC, Tsai WC, Chen HH. RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes. BMC PLANT BIOLOGY 2019; 19:337. [PMID: 31375064 PMCID: PMC6679452 DOI: 10.1186/s12870-019-1940-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/17/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
| | - Oh Keun Kwon
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Yun Su Baek
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Byoung-Chorl Kang
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Wen-Chieh Tsai
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Chen Y, Wang Y, Lyu P, Chen L, Shen C, Sun C. Comparative transcriptomic analysis reveal the regulation mechanism underlying MeJA-induced accumulation of alkaloids in Dendrobium officinale. JOURNAL OF PLANT RESEARCH 2019. [PMID: 30903398 DOI: 10.1007/s10265-019-01099-6/1618-0860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale.
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Affiliation(s)
- Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Yunzhu Wang
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Ping Lyu
- Lin'an Agricultural and Forestry Technology Extension Center, Hangzhou, Zhejiang, People's Republic of China
| | - Liping Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China.
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China.
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Chen Y, Wang Y, Lyu P, Chen L, Shen C, Sun C. Comparative transcriptomic analysis reveal the regulation mechanism underlying MeJA-induced accumulation of alkaloids in Dendrobium officinale. JOURNAL OF PLANT RESEARCH 2019; 132:419-429. [PMID: 30903398 DOI: 10.1007/s10265-019-01099-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale.
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Affiliation(s)
- Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Yunzhu Wang
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Ping Lyu
- Lin'an Agricultural and Forestry Technology Extension Center, Hangzhou, Zhejiang, People's Republic of China
| | - Liping Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China.
- Key Laboratory of Creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China.
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Kabacaoğlu E, Budak BK. Detection and quantification of salep with real time PCR utilizing the nr-ITS2 region. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2447-2454. [PMID: 30362130 DOI: 10.1002/jsfa.9453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/14/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Salep is a highly valued food product, susceptible to adulteration with less costly additives such as starch. The aim of this study is to develop a real-time polymerase chain reaction (PCR) method for the detection and quantification of authentic salep using primers designed from the nr-ITS2 region. RESULTS The designed primers were shown to amplify selectively with salep DNA and cloning/sequencing of end-point PCR products obtained with authentic salep (Orchideceae) confirmed amplimers to be copies of the intended target region. Detection of salep DNA using the designed primer set was possible at levels as low as 20 pg. After initial evaluation of the real-time PCR method with binary DNA mixtures of salep and cornflour, quantification of salep was conducted in binary mixtures of potato starch (a more likely adulterant) and salep, showing that quantification within the range 25%-100% could be achieved. The real-time assay was performed using the 18S rDNA region co-amplified as an internal standard and evaluated using the ΔΔCt method. The calibration curves obtained as a result of real-time PCR runs showed linearity, with R2 values above 99%. CONCLUSION A real-time PCR method using SybreGreen intercalating dye was established for salep detection and quantification based on the specific amplification of salep DNA. Method validation was performed utilizing blind and commercial samples. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Eda Kabacaoğlu
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Barçın Karakaş Budak
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
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Rewicz A, Rewers M, Jędrzejczyk I, Rewicz T, Kołodziejek J, Jakubska-Busse A. Morphology and genome size of Epipactis helleborine (L.) Crantz (Orchidaceae) growing in anthropogenic and natural habitats. PeerJ 2018; 6:e5992. [PMID: 30595975 PMCID: PMC6304265 DOI: 10.7717/peerj.5992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/23/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to (i) determine and compare the phenotypic variation of E. helleborine (L.) Crantz plants in anthropogenic and natural habitats, (ii) compare the genome size of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species. METHODS Field studies were conducted on four native stands and four stands in anthropogenic areas of E. helleborine in Poland in years 2011-2013. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 programme (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from four natural and four anthropogenic populations. RESULTS We observed that in anthropogenic populations: (i) shoots were higher than shoots from natural populations, (ii) flowers differed significantly in terms of ten biometric features between habitats, (iii) the genome size of some population differed significantly between plants growing in natural and anthropogenic habitats. DISCUSSION According to some researchers, the presence of phenotypic variability and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features, i.e., high shoots, long inflorescence and long, broad leaves. We agree, however, that it is difficult to isolate a taxonomic unit for ecofen due to the lack of experimental research.
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Affiliation(s)
- Agnieszka Rewicz
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Monika Rewers
- Department of Agricultural Biotechnology, UTP University of Science and Technology, Laboratory of Molecular Biology and Cytometry, Bydgoszcz, Poland
| | - Iwona Jędrzejczyk
- Department of Agricultural Biotechnology, UTP University of Science and Technology, Laboratory of Molecular Biology and Cytometry, Bydgoszcz, Poland
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Jeremi Kołodziejek
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Anna Jakubska-Busse
- Department of Botany, Institute of Environmental Biology, University of Wrocław, Wrocław, Poland
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Hu C, Yang H, Jiang K, Wang L, Yang B, Hsieh T, Lan S, Huang W. Development of polymorphic microsatellite markers by using de novo transcriptome assembly of Calanthe masuca and C. sinica (Orchidaceae). BMC Genomics 2018; 19:800. [PMID: 30400862 PMCID: PMC6219035 DOI: 10.1186/s12864-018-5161-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/11/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest China. Both play important roles in horticulture and are under the pressure of population decline. Understanding their genetic background can greatly help us develop effective conservation strategies for these species. Simple sequence repeats (SSRs) are useful for genetic diversity analysis, presumably providing key information for the study and preservation of the wild populations of the two species we are interested in. RESULTS In this study, we performed RNA-seq analysis on the leaves of C. masuca and C. sinica, obtaining 40,916 and 71,618 unigenes for each species, respectively. In total, 2,019/3,865 primer pairs were successfully designed from 3,764/7,189 putative SSRs, among which 197 polymorphic SSRs were screened out according to orthologous gene pairs. After mononucleotide exclusion, a subset of 129 SSR primers were analysed, and 13 of them were found to have high polymorphism levels. Further analysis demonstrated that they were feasible and effective against C. masuca and C. sinica as well as transferable to another species in Calanthe. Molecular evolutionary analysis revealed functional pathways commonly enriched in unigenes with similar evolutionary rates in the two species, as well as pathways specific to each species, implicating species-specific adaptation. The divergence time between the two closely related species was tentatively determined to be 3.42 ± 1.86 Mya. CONCLUSIONS We completed and analysed the transcriptomes of C. masuca and C. sinica, assembling large numbers of unigenes and generating effective polymorphic SSR markers. This is the first report of the development of expressed sequence tag (EST)-SSR markers for Calanthe. In addition, our study could enable further genetic diversity analysis and functional and comparative genomic studies on Calanthe.
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Affiliation(s)
- Chao Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hongxing Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Kai Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Ling Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
| | - Boyun Yang
- School of Life Science, Nanchang University, Nanchang, 330031 China
| | - Tungyu Hsieh
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Siren Lan
- College of Landscape, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weichang Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602 China
- College of Landscape, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Roma L, Cozzolino S, Schlüter PM, Scopece G, Cafasso D. The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids. PLoS One 2018; 13:e0204174. [PMID: 30226857 PMCID: PMC6143245 DOI: 10.1371/journal.pone.0204174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022] Open
Abstract
Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus.
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Affiliation(s)
- Luca Roma
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Salvatore Cozzolino
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- * E-mail:
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
- Institute of Botany, University of Hohenheim, Garbenstraße 30, Stuttgart, Germany
| | - Giovanni Scopece
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Donata Cafasso
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
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Bateman RM, Guy JJ, Rudall PJ, Leitch IJ, Pellicer J, Leitch AR. Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids. ANNALS OF BOTANY 2018; 122:133-150. [PMID: 29672665 PMCID: PMC6025197 DOI: 10.1093/aob/mcy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/15/2018] [Indexed: 05/07/2023]
Abstract
Background and Aims Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication. Key Results In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication. Conclusions Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.
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Affiliation(s)
| | - Jessica J Guy
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC. Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:631-640. [PMID: 29608785 DOI: 10.1002/ajb2.1047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
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Affiliation(s)
- Sarah A Unruh
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung 404, Taiwan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Science Museum, Amakubo, Tsukuba, 305-0005, Japan
| | | | - Richard P Shefferson
- Organization for Programs on Environmental Sciences, University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Ann Smithson
- Smithson Environmental Consultancy & DNALabs Environmental Genetics Testing, Bassendean, Western Australia, 6054
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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41
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Bateman RM, Sramkó G, Paun O. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids. ANNALS OF BOTANY 2018; 121:85-105. [PMID: 29325077 PMCID: PMC5786241 DOI: 10.1093/aob/mcx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/02/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. METHODS At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. KEY RESULTS RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. CONCLUSIONS The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.
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Affiliation(s)
- Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
- For correspondence. E-mail
| | - Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Egyetem, Debrecen, Hungary
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg, Vienna, Austria
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Yagi M. Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants. BREEDING SCIENCE 2018; 68:62-70. [PMID: 29681748 PMCID: PMC5903975 DOI: 10.1270/jsbbs.17080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/19/2017] [Indexed: 05/21/2023]
Abstract
Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation. Genome-related research in ornamentals plants has been relatively slow to develop because of their heterozygosity or polyploidy. Advances in analytical instruments, such as next-generation sequencers and information processing technologies have revolutionized biology, and have been applied in a large number and variety of species, including ornamental plants. Recently, high-quality whole genome sequences have been reported in plant genetics and physiology studies of model ornamentals, such as those in genus Petunia and Japanese morning glory (Ipomoea nil). In this review, whole genome sequencing and construction of high-density genetic linkage maps based on SNP markers of ornamentals will be discussed. The databases that store this information for ornamentals are also described.
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43
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. The Apostasia genome and the evolution of orchids. Nature 2017; 549:379-383. [PMID: 28902843 PMCID: PMC7416622 DOI: 10.1038/nature23897] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica4, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
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Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
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Štubňová E, Hodálová I, Kučera J, Mártonfiová L, Svitok M, Slovák M. Karyological patterns in the European endemic genus Soldanella L.: Absolute genome size variation uncorrelated with cytotype chromosome numbers. AMERICAN JOURNAL OF BOTANY 2017; 104:1241-1253. [PMID: 28790087 DOI: 10.3732/ajb.1700153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Detailed knowledge about the karyological diversity of organisms undoubtedly represents one of the crucial steps toward a better understanding of their evolutionary trends and history. We investigated the cytotype and absolute genome size (AGS) patterns in the European mountain-dwelling genus Soldanella (Primulaceae) in light of its geographic distribution and ecological diversification. METHODS Our chromosome number survey was based on 34 newly determined and 125 previously published chromosome counts. AGS was estimated on the basis of propidium iodide (PI) flow cytometry (299 individuals, 110 populations). KEY RESULTS We confirmed the existence of two cytotypes with the same ploidy level, i.e., euploid 2n = 40 and dysploid 2n = 38. The overall infrageneric AGS variation ranged between 2.97 and 3.99 pg (25.6% variation). The 2n = 40 cytotype harbors a modest amount of continuous AGS variation. With regard to its distribution area and ecology, the cytotype is ubiquitous. By contrast, the 2n = 38 cytotype was detected only in six forest-dwelling taxa with AGS variation segregated into three discrete, geographically separated groups. The AGS variation of the 2n = 38 cytotype was strongly correlated with elevation and longitude. CONCLUSIONS Despite the apparent morphological and ecological variation, members of the genus Soldanella have not undergone any pronounced cytotype and AGS diversification during their evolutionary history. The lack of correlation between chromosome numbers and AGS indicates that the evolutionary mechanism behind the origin of the dysploid cytotype 2n = 38 was a chromosomal fusion.
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Affiliation(s)
- Eliška Štubňová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Iva Hodálová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Jaromír Kučera
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Lenka Mártonfiová
- Pavol Jozef Šafárik University, Botanical Garden, Mánesova 23, SK-04352 Košice, Slovak Republic
| | - Marek Svitok
- Technical University, Faculty of Ecology, T. G. Masaryka 2117/24, SK-96053 Zvolen, Slovak Republic
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
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Du YP, Bi Y, Zhang MF, Yang FP, Jia GX, Zhang XH. Genome Size Diversity in Lilium (Liliaceae) Is Correlated with Karyotype and Environmental Traits. FRONTIERS IN PLANT SCIENCE 2017; 8:1303. [PMID: 28798759 PMCID: PMC5526928 DOI: 10.3389/fpls.2017.01303] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/11/2017] [Indexed: 05/25/2023]
Abstract
Genome size (GS) diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood. We performed a comprehensive study involving phylogenetically independent analysis on 71 species to explore the diversity and evolution of GS and its correlation with karyological and environmental traits within Lilium (including Nomocharis). The strong phylogenetic signal detected for GS in the genus provides evidence consistent with that the repetitive DNA may be the primary contributors to the GS diversity, while the significant positive relationships detected between GS and the haploid chromosome length (HCL) provide insights into patterns of genome evolution. The relationships between GS and karyotypes indicate that ancestral karyotypes of Lilium are likely to have exhibited small genomes, low diversity in centromeric index (CVCI) values and relatively high relative variation in chromosome length (CVCL) values. Significant relationships identified between GS and annual temperature and between GS and annual precipitation suggest that adaptation to habitat strongly influences GS diversity. We conclude that GS in Lilium is shaped by both neutral (genetic drift) and adaptive evolution. These findings will have important consequences for understanding the evolution of giant plant genomes, and exploring the role of repetitive DNA fraction and chromosome changes in a plant group with large genomes and conservation of chromosome number.
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Affiliation(s)
- Yun-peng Du
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Engineering Technology Research Center of Functional FloricultureBeijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Yu Bi
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Engineering Technology Research Center of Functional FloricultureBeijing, China
| | - Ming-fang Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Engineering Technology Research Center of Functional FloricultureBeijing, China
| | - Feng-ping Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Engineering Technology Research Center of Functional FloricultureBeijing, China
| | - Gui-xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Xiu-hai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Engineering Technology Research Center of Functional FloricultureBeijing, China
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47
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Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodeling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2-32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.
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Affiliation(s)
- Spencer C. Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia,
France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion – Cirad, Pôle de Protection des
Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech,
Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS,
INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université
Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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Moraes AP, Koehler S, Cabral JS, Gomes SSL, Viccini LF, Barros F, Felix LP, Guerra M, Forni-Martins ER. Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:298-308. [PMID: 27917576 DOI: 10.1111/plb.12527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution. To do so, the GS (14 species), the karyotype - based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) - was characterised and analysed along with published data using phylogenetic approaches. The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants - higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number. Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.
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Affiliation(s)
- A P Moraes
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Brazil
- Instituto de Ciências e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - S Koehler
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
| | - J S Cabral
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
- Synthesis Centre, German Centre for Integrative Biodiversity Research, Leipzig, Germany
- Center for Computational and Theoretical Biology, Ecosystem Modeling, University of Würzburg, Würzburg, Germany
| | - S S L Gomes
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - L F Viccini
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - F Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado de São Paulo, São Paulo, Brazil
| | - L P Felix
- Departamento de Ciências Biológicas, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Rodovia, Areias, Brazil
| | - M Guerra
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
| | - E R Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
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Bateman RM, Molnár V A, Sramkó G. In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae). PeerJ 2017; 5:e2893. [PMID: 28168103 PMCID: PMC5289109 DOI: 10.7717/peerj.2893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022] Open
Abstract
Background and Aims The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade. Methods Between one and 12 plants found in 25 populations that encompassed the entire distribution of the Himantoglossum s.l. clade were measured in situ for 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses. Key Results Multivariate analyses readily separate subgenus Barlia and subgenus Comperia from subgenus Himantoglossum, and also the early-divergent H. formosum from the less divergent remainder of subgenus Himantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution within Himantoglossum is unusually multi-dimensional. Conclusions Degrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses. Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenus Himantoglossum—hircinum, caprinum and formosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separate bona fide species. All taxa achieve allogamy via food deceit and have only weak pollinator specificity. Artificial crossing demonstrates that intrinsic sterility barriers are weak. Although we have found evidence of gene flow among and within the three sections of subgenus Himantoglossum, reports of natural hybrids are surprisingly rare, probably because putative parents are sufficiently similar to questionably warrant the status of species. Phenological separation and increased xeromorphy characterise the origin of subgenus Barlia. Several individual morphological characters show evidence of parallel acquisition, and loss of features is especially frequent in floral markings among members of section caprinum. Detailed patterns of gain and loss demonstrate that several different categories of flower markings are inherited independently. Along with the dimensions of labellar lobes, these pigmentation characters have been over-emphasised in previous taxonomic treatments. Increased plant vigour was a crucial element of the origin of the genus, but vegetative characters underwent remarkably little subsequent evolution. Attempts to reconstruct hypothetical ancestors at internal nodes of the phylogeny are weakened by (a) uncertain placement of Steveniella as sister to Himantoglossum s.l. and (b) uncertain relationships among subtly different putative species within section caprinum. Nonetheless, heterochronic/allometric trends, ultimately limited by functional constraints, clearly dictate transitions between contrasting flower sizes and complex labellum shapes.
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Affiliation(s)
| | - Attila Molnár V
- Department of Botany, University of Debrecen , Debrecen , Hungary
| | - Gábor Sramkó
- Department of Botany, University of Debrecen, Debrecen, Hungary; MTA-DE "Lendület" Evolutionary Phylogenomics Research Group, Debrecen, Hungary
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50
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Hoshi Y, Azumatani M, Suyama C, Adamec L. Determination of Ploidy Level and Nuclear DNA Content in the Droseraceae by Flow Cytometry. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University
| | | | - Chika Suyama
- Science Education (Biology), Faculty of Education, Gifu University
| | - Lubomίr Adamec
- Section of Plant Ecology, Institute of Botany of the Czech Academy of Sciences
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