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Tao K, Tao L, Huang J, Duan H, Luo Y, Li L. Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata. BMC Genomics 2024; 25:552. [PMID: 38825700 PMCID: PMC11145882 DOI: 10.1186/s12864-024-10458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND The disputed phylogenetic position of Aerides flabellata Rolfe ex Downie, due to morphological overlaps with related species, was investigated based on evidence of complete chloroplast (cp) genomes. The structural characterization of complete cp genomes of A. flabellata and A. rosea Lodd. ex Lindl. & Paxton were analyzed and compared with those of six related species in "Vanda-Aerides alliance" to provide genomic information on taxonomy and phylogeny. RESULTS The cp genomes of A. flabellata and A. rosea exhibited conserved quadripartite structures, 148,145 bp and 147,925 bp in length, with similar GC content (36.7 ~ 36.8%). Gene annotations revealed 110 single-copy genes, 18 duplicated in inverted regions, and ten with introns. Comparative analysis across related species confirmed stable sequence identity and higher variation in single-copy regions. However, there are notable differences in the IR regions between two Aerides Lour. species and the other six related species. The phylogenetic analysis based on CDS from complete cp genomes indicated that Aerides species except A. flabellata formed a monophyletic clade nested in the subtribe Aeridinae, being a sister group to Renanthera Lour., consistent with previous studies. Meanwhile, a separate clade consisted of A. flabellata and six Vanda R. Br. species was formed, as a sister taxon to Holcoglossum Schltr. CONCLUSIONS This research was the first report on the complete cp genomes of A. flabellata. The results provided insights into understanding of plastome evolution and phylogenetic relationships of Aerides. The phylogenetic analysis based on complete cp genomes showed that A. flabellata should be placed in Vanda rather than in Aerides.
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Affiliation(s)
- Kaifeng Tao
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Lei Tao
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Jialin Huang
- School of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, Yunnan, 653100, China
| | - Hanning Duan
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yan Luo
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
| | - Lu Li
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China.
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Ma L, Zhou CY, Chen JL, Liu DK, Lan S, Liu ZJ. Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation. Genes (Basel) 2023; 15:20. [PMID: 38254910 PMCID: PMC10815154 DOI: 10.3390/genes15010020] [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: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia.
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Affiliation(s)
- Liang Ma
- Fujian Health College, Fuzhou 350101, China;
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Cheng-Yuan Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Jin-Liao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
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Chen J, Wang F, Zhou C, Ahmad S, Zhou Y, Li M, Liu Z, Peng D. Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes. Int J Mol Sci 2023; 24:12473. [PMID: 37569853 PMCID: PMC10420012 DOI: 10.3390/ijms241512473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/04/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes and colors. Although the morphological boundaries of Aerides are clearly defined, the relationship between Aerides and other closely related genera is still ambiguous in terms of phylogeny. To better understand their phylogenetic relationships, this study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of this taxonomic unit using genetic information from six Aerides plastid genomes. The quadripartite-structure plastomes ranged from 147,244 bp to 148,391 bp and included 120 genes. Among them, 74 were protein coding genes, 38 were tRNA genes and 8 were rRNA genes, while the ndh genes were pseudogenized or lost. Four non-coding mutational hotspots (rpl20-rpl33, psbM, petB, rpoB-trnCGCA, Pi > 0.06) were identified. A total of 71-77 SSRs and 19-46 long repeats (>30 bp) were recognized in Aerides plastomes, which were mostly located in the large single-copy region. Phylogenetic analysis indicated that Aerides was monophylic and sister to Renanthera. Moreover, our results confirmed that six Aerides species can be divided into three major clades. These findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contributes to future research on the phylogenomics of Orchidaceae.
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Affiliation(s)
| | | | | | | | | | | | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Chen J, Wang F, Zhao Z, Li M, Liu Z, Peng D. Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species. Int J Mol Sci 2023; 24:11167. [PMID: 37446345 DOI: 10.3390/ijms241311167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of Paraphalaenopsis (P. labukensis, P. denevel, and P. laycockii 'Semi-alba') and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (psbM-trnDGUC, psbB, ccsA, trnKUUU, trnSGCU-trnGUCC, rps16-trnQUUG) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that Paraphalaenopsis was a clade of Aeridinae that was sister to the Holcoglossum-Vanda clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae.
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Affiliation(s)
- Jinliao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fei Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minghe Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Feng Y, Gao XF, Zhang JY, Jiang LS, Li X, Deng HN, Liao M, Xu B. Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of Campylotropis (Fabaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:895543. [PMID: 35665174 PMCID: PMC9158520 DOI: 10.3389/fpls.2022.895543] [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: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 06/03/2023]
Abstract
The genus Campylotropis Bunge (Desmodieae, Papilionoideae) comprises about 37 species distributed in temperate and tropical Asia. Despite the great potential in soil conservation, horticulture, and medicine usage, little is known about the evolutionary history and phylogenetic relationships of Campylotropis due to insufficient genetic resources. Here, we sequenced and assembled 21 complete chloroplast genomes of Campylotropis species. In combination with the previously published chloroplast genomes of C. macrocarpa and closely related species, we conducted comparative genomics and phylogenomic analysis on these data. Comparative analysis of the genome size, structure, expansion and contraction of inverted repeat (IR) boundaries, number of genes, GC content, and pattern of simple sequence repeats (SSRs) revealed high similarities among the Campylotropis chloroplast genomes. The activities of long sequence repeats contributed to the variation in genome size and gene content in Campylotropis chloroplast genomes. The Campylotropis chloroplast genomes showed moderate sequence variation, and 13 highly variable regions were identified for species identification and further phylogenetic studies. We also reported one more case of matK pseudogene in the legume family. The phylogenetic analysis confirmed the monophyly of Campylotropis and the sister relationship between Lespedeza and Kummerowia, the latter two genera were then sister to Campylotropis. The intrageneric relationships of Campylotropis based on genomic scale data were firstly reported in this study. The two positively selected genes (atpF and rps19) and eight fast-evolving genes identified in this study may help us to understand the adaptation of Campylotropis species. Overall, this study enhances our understanding of the chloroplast genome evolution and phylogenetic relationships of Campylotropis.
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Affiliation(s)
- Yu Feng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Li-Sha Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiong Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Heng-Ning Deng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Min Liao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Mangkang Ecological Station, Tibet Ecological Safety Monitor Network, Changdu, China
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Thant MT, Sritularak B, Chatsumpun N, Mekboonsonglarp W, Punpreuk Y, Likhitwitayawuid K. Three Novel Biphenanthrene Derivatives and a New Phenylpropanoid Ester from Aerides multiflora and Their α-Glucosidase Inhibitory Activity. PLANTS (BASEL, SWITZERLAND) 2021; 10:385. [PMID: 33671404 PMCID: PMC7922108 DOI: 10.3390/plants10020385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/18/2022]
Abstract
A phytochemical investigation on the whole plants of Aerides multiflora revealed the presence of three new biphenanthrene derivatives named aerimultins A-C (1-3) and a new natural phenylpropanoid ester dihydrosinapyl dihydroferulate (4), together with six known compounds (5-10). The structures of the new compounds were elucidated by analysis of their spectroscopic data. All of the isolates were evaluated for their α-glucosidase inhibitory activity. Aerimultin C (3) showed the most potent activity. The other compounds, except for compound 4, also exhibited stronger activity than the positive control acarbose. Compound 3 showed non-competitive inhibition of the enzyme as determined from a Lineweaver-Burk plot. This study is the first phytochemical and biological investigation of A. multiflora.
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Affiliation(s)
- May Thazin Thant
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (M.T.T.); (K.L.)
- Department of Pharmacognosy, University of Pharmacy, Yangon 11031, Myanmar
| | - Boonchoo Sritularak
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (M.T.T.); (K.L.)
- Natural Products for Ageing and Chronic Diseases Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nutputsorn Chatsumpun
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand;
| | - Wanwimon Mekboonsonglarp
- Scientific and Technological Research Equipment Centre, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Yanyong Punpreuk
- Department of Agriculture, Kasetsart University, Bangkok 10900, Thailand;
| | - Kittisak Likhitwitayawuid
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (M.T.T.); (K.L.)
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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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Kim YK, Jo S, Cheon SH, Kwak M, Kim YD, Kim KJ. Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae). Mol Phylogenet Evol 2019; 144:106721. [PMID: 31870921 DOI: 10.1016/j.ympev.2019.106721] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 02/03/2023]
Abstract
Subtribe Aeridinae (Vandeae, Epidendroideae, Orchidaceae) consists of 83 genera and 2,345 species. The present study completely decoded the plastomes and nuclear ribosomal (nr) RNA gene clusters of seven species of Aeridinae belonging to Gastrochilus, Neofinetia, Pelatantheria, and Thrixspermum and compared them with existing data to investigate their genome evolution and phylogeny. Although no large structural variations were observed among the Aeridinae plastomes, 14 small inversions (SI) were found in Orchidaceae for the first time. Therefore, the evolutionary trends and usefulness of SI as molecular identification markers were evaluated. Since all 11 ndh genes in the Aeridinae plastome were lost or pseudogenized, the evolutionary trends of ndh genes are discussed at the tribe and family levels. In the maximum likelihood tree reconstructed from 83 plastome genes, the five Orchidaceae subfamilies were shown to have diverged in the following order: Apostasioideae, Vanilloideae, Cypripedioideae, Orchioideae, Epidendroideaeae. Divergence times for major lineages were found to be more recent, 5-10 Mya, than previous studies, which only used two or three genes. Vandeae, which includes Aeridinae, formed a sister group with Cymbidieae and Epidendreae. The Vandeae, Cymbidieae, and Epidendreae lineages were inferred to have diverged at 25.31 Mya; thus, numerous speciation events within Aeridineae occurred since then. Furthermore, the present study reconstructed a phylogenetic tree from 422 nrITS sequences belonging to Aerdinae and allied taxa and uses it to discuss the phylogenetic positions and species identities of five endangered species.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Myounghai Kwak
- Department of Plant Resources, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon 24252, Republic of Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
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Kishor R, Sharma GJ. The use of the hypervariable P8 region of trnL(UAA) intron for identification of orchid species: Evidence from restriction site polymorphism analysis. PLoS One 2018; 13:e0196680. [PMID: 29718976 PMCID: PMC5931654 DOI: 10.1371/journal.pone.0196680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022] Open
Abstract
The P8 stem-loop region of the trnL intron, which is known to be hypervariable in size with multiple repeat motifs and created difficulties in alignment, is always excluded in phylogenetic as well as barcode analyses. This region was investigated for species discrimination in 98 taxa of orchids belonging to the tribe Vandeae using in silico mapping of restriction site polymorphism. The length of the P8 regions varied from 200 nucleotides in Aerides rosea to 669 nucleotides in Dendrophylax sallei. Forty two taxa had unique lengths, while as many as eight shared a common length of 521 nucleotides. Of the 35 restriction endonucleases producing digestions in the P8 regions, three, viz., AgsI, ApoI and TspDTI turned out to have recognition sites across all the 98 taxa being studied. When their restriction data were combined, 92 taxa could be discriminated leaving three taxon pairs. However, Acampe papillosa and Aeranthes arachnites despite having similar restriction sites differed in their P8 lengths. This is the first report on thorough investigation of the P8 region of trnL intron for search of species specific restriction sites and hence its use as a potential plant DNA barcode.
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Affiliation(s)
- Rajkumar Kishor
- Department of Life Sciences, Manipur University, Imphal, Manipur, India
- * E-mail:
| | - G. J. Sharma
- Department of Life Sciences, Manipur University, Imphal, Manipur, India
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Ponert J, Trávníček P, Vuong TB, Rybková R, Suda J. A New Species of Cleisostoma (Orchidaceae) from the Hon Ba Nature Reserve in Vietnam: A Multidisciplinary Assessment. PLoS One 2016; 11:e0150631. [PMID: 27008538 PMCID: PMC4805174 DOI: 10.1371/journal.pone.0150631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/16/2016] [Indexed: 11/22/2022] Open
Abstract
A new species, Cleisostoma yersinii J. Ponert & Vuong, is described and illustrated based on the material collected in the Hon Ba Nature Reserve in southern Vietnam. In addition to conventional (macro)morphological examination we comparatively investigated root and leaf anatomy (using light and fluorescent microscopy), assessed nectar characteristics (using HPLC analysis), determined nuclear genome size (using DNA flow cytometry) and reconstructed phylogenetic relationships (using nrITS sequences). Cleisostoma yersinii differs from its putative closest relative C. birmanicum in wider and shorter leaves, larger flowers, distinct lip with S-shaped tip of the mid-lobe, and a shallow spur with two large nectar sacks separated by prominent calli and septum. Nectar is sucrose-dominant and very rich in sugars. Stomata are developed on both sides of the leaf and have prominent hyperstomatal chambers and substomatal cavities. Roots with well-developed exodermis and tracheoidal idioblasts are covered by a two-layer Vanda-type velamen. Chloroplasts occur not only in the cortex but are also abundant in the stele. Mean 1C-value was estimated to 2.57 pg DNA. An updated identification key is provided for SE Asian sections and all Vietnamese species of Cleisostoma.
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Affiliation(s)
- Jan Ponert
- Prague Botanical Garden, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| | - Pavel Trávníček
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Truong Ba Vuong
- Institute of Tropical Biology, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | | | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015. [PMID: 26416561 DOI: 10.1186/s12862-015-0491-491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015; 15:210. [PMID: 26416561 PMCID: PMC4587860 DOI: 10.1186/s12862-015-0491-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/20/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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Zou LH, Huang JX, Zhang GQ, Liu ZJ, Zhuang XY. A molecular phylogeny of Aeridinae (Orchidaceae: Epidendroideae) inferred from multiple nuclear and chloroplast regions. Mol Phylogenet Evol 2015; 85:247-54. [DOI: 10.1016/j.ympev.2015.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 01/06/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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Cakova V, Urbain A, Antheaume C, Rimlinger N, Wehrung P, Bonté F, Lobstein A. Identification of phenanthrene derivatives in Aerides rosea (Orchidaceae) using the combined systems HPLC-ESI-HRMS/MS and HPLC-DAD-MS-SPE-UV-NMR. PHYTOCHEMICAL ANALYSIS : PCA 2015; 26:34-39. [PMID: 25130411 DOI: 10.1002/pca.2533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/07/2014] [Accepted: 06/22/2014] [Indexed: 06/03/2023]
Abstract
INTRODUCTION In our continued efforts to contribute to the general knowledge on the chemical diversity of orchids, we have decided to focus our investigations on the Aeridinae subtribe. Following our previous phytochemical study of Vanda coerulea, which has led to the identification of phenanthrene derivatives, a closely related species, Aerides rosea Lodd. ex Lindl. & Paxton, was chosen for investigation. OBJECTIVE To identify new secondary metabolites, and to avoid isolation of those already known, by means of the combined systems HPLC-DAD(diode-array detector) with high-resolution tandem mass spectrometry (HRMS/MS) and HPLC-DAD-MS-SPE(solid-phase extraction)-UV-NMR. METHODS A dereplication strategy was developed using a HPLC-DAD-HRMS/MS targeted method and applied to fractions from A. rosea stem extract. Characterisation of unknown minor compounds was then performed using the combined HPLC-DAD-MS-SPE-UV-NMR system. RESULTS The dereplication method allowed the characterisation of four compounds (gigantol, imbricatin, methoxycoelonin and coelonin), previously isolated from Vanda coerulea stem extract. The analyses of two fractions permitted the identification of five additional minor constituents including one phenanthropyran, two phenanthrene and two dihydrophenanthrene derivatives. The full set of NMR data of each compound was obtained from microgram quantities. CONCLUSION Nine secondary metabolites were characterised in A. rosea stems, utilising HPLC systems combined with high-resolution analytical systems. Two of them are newly described phenanthrene derivatives: aerosanthrene (5-methoxyphenanthrene-2,3,7-triol) and aerosin (3-methoxy-9,10-dihydro-2,5,7-phenanthrenetriol).
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Affiliation(s)
- Veronika Cakova
- University of Strasbourg, Faculty of Pharmacy, Laboratory of Pharmacognosy and Bioactive Natural Products, 74, route du Rhin, CS60024, 67400, Illkirch Graffenstaden, France; LVMH recherche, 185 avenue de Verdun, 45800, Saint Jean de Braye, France
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Zhang GQ, Liu KW, Chen LJ, Xiao XJ, Zhai JW, Li LQ, Cai J, Hsiao YY, Rao WH, Huang J, Ma XY, Chung SW, Huang LQ, Tsai WC, Liu ZJ. A new molecular phylogeny and a new genus, Pendulorchis, of the Aerides-Vanda alliance (Orchidaceae: Epidendroideae). PLoS One 2013; 8:e60097. [PMID: 23577083 PMCID: PMC3618120 DOI: 10.1371/journal.pone.0060097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 02/24/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Aerides-Vanda alliance is a complex group in the subtribe Aeridinae (subfamily Epidendroideae, Orchidaceae). Some phylogenetic systems of this alliance have been previously proposed based on molecular and morphological analyses. However, several taxonomic problems within this alliance as well as between it and its allies remain unsolved. METHODOLOGY/PRINCIPAL FINDINGS We utilized ITS and five plastid DNA regions in this phylogenetic analysis. Consensus trees strongly indicate that the Aerides-Vanda alliance is monophyletic, and the 14 genera of this alliance can be grouped into the following clades with 14 subclades: 1. Aerides, comprising two subclades: Rhynchostylis and Aerides; 2. Ascocentropsis; 3. Papilionanthe; 4. Vanda, comprising five subclades: Neofinetia, Christensonia, Seidenfadenia, Ascocentrum, and Vanda-Trudelia, in which Vanda and Trudelia form a subclade; 5. Tsiorchis, comprising three subclades: Chenorchis, Tsiorchis, and two species of Ascocentrum; 6. Paraholcoglossum; and 7. Holcoglossum. Among the 14 genera, only Ascocentrum is triphyletic: two species of the Ascocentrum subclade, an independent subclade Ascocentrum subclade in the Tsiorchis clade; the Ascocentrum subclade in the Vanda clade; and one species in the Holcoglossum clade. The Vanda and Trudelia species belong to the same subclade. The molecular conclusion is consistent with their morphological characteristics. CONCLUSIONS We elucidate the relationship among the 14 genera of the Aerides-Vanda alliance. Our phylogenetic results reveal that the Aerides-Vanda alliance is monophyletic, but it can be divided into 14 genera. The data prove that Ascocentrum is triphyletic. Plants with elongate-terete leaves and small flowers should be treated as a new genus, Pendulorchis. Saccolabium himalaicum (Ascocentrum himalaicum) should be transferred to Pendulorchis. Ascocentrum pumilum, endemic to Taiwan, should be transferred to Holcoglossum. A new combination, Holcoglossum pumilum, was also established. Trudelia should not be recognized as an independent genus. Two new species, Pendulorchis gaoligongensis and Holcoglossum singchianum, were described as well.
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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, China
- Landscape College of Fujian Agriculture and Forestry University, Fuzhou, 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, China
- The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 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, 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, China
| | - Jun-Wen Zhai
- 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, China
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Li-Qiang Li
- 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, China
| | - Jing Cai
- 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, China
| | - Yu-Yun Hsiao
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Wen-Hui Rao
- 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, China
| | - Jie 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, China
| | - Xue-Yong Ma
- 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, China
| | - Shih-Wen Chung
- Department of Botany, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Lai-Qiang Huang
- The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Orchid Research Center, National Cheng Kung University, Tainan City, Taiwan
- * E-mail: (ZJL); (WCT)
| | - 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, China
- The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
- College of Forestry, South China Agricultural University, Guangzhou, China
- Landscape College of Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (ZJL); (WCT)
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Xiang X, Li D, Jin X, Hu H, Zhou H, Jin W, Lai Y. Monophyly or paraphyly--the taxonomy of Holcoglossum (Aeridinae: Orchidaceae). PLoS One 2012; 7:e52050. [PMID: 23251681 PMCID: PMC3522637 DOI: 10.1371/journal.pone.0052050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/08/2012] [Indexed: 11/20/2022] Open
Abstract
Recently, there have been a lot of intense debates about the acceptance/rejection of paraphyletic groups in biological classification. On the one hand, evolutionary classification states that similarity and common descent are two criteria for biological classification and paraphyletic groups are natural units of biological classification. On the other hand, cladistic classification considers that common descent is the only criterion in biological classification and monophyly should be strictly adhered to. Holcoglossum is used herein as a case to illustrate this problem. Although Holcoglossum is a small orchid genus of less than 20 species, there is little consensus about its generic circumscription since it was established, which leads to confusion in taxonomic treatments in the Aerides-Vanda group. Based on the analyses of molecular and morphological evidence, our results suggest that the clade comprising Holcoglossum s.s., Ascolabium, Penkimia and Ascocentrum himalaicum is strongly supported as a monophyly, and that the three taxa are nested within different subclades of Holcoglossum s.s. Thus, it is reasonable to recognize a monophyletic circumscription of Holcoglossum, which is also well supported by some vegetative and floral characters. The Holcoglossum s.l. would facilitate a better understanding of pollinator-driven floral divergence and vegetative stasis than a paraphyletic and narrowly defined genus.
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Affiliation(s)
- Xiaoguo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Xiaohua J, Dezhu L, Zongxin R, Xiaoguo X. A generalized deceptive pollination system of Doritis pulcherrima (Aeridinae: Orchidaceae) with non-reconfigured pollinaria. BMC PLANT BIOLOGY 2012; 12:67. [PMID: 22571550 PMCID: PMC3388949 DOI: 10.1186/1471-2229-12-67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 05/09/2012] [Indexed: 05/11/2023]
Abstract
BACKGROUND As one of largest angiosperm families, orchids have long fascinated evolutionary biologists with their staggering diversity in floral design and display to promote outcrossing. Two of the most intriguing aspects of orchid pollination that promote cross-pollination are pollinarium reconfiguration (PR) and deceptive pollination. PR and generalized food deception employ virtually antagonistic methods of promoting cross-pollination: PR occurs through delayed pollination, involving the relatively long visitation periods that are typically observed for the pollinators of one flower or inflorescence; conversely, generalized food deception leads to reductions in the visitation periods of pollinators to one flower or inflorescence. Thus, it is logical to hypothesize that PR is unnecessary or PR happens soon in generalized food-deceptive orchids in the promotion of cross-pollination. Using Doritis pulcherrima as a model, the aim of this study was to understand the following: (1) the pollination and breeding system of D. pulcherrima; (2) the morphological interactions between orchids and their pollinators; and (3) whether PR is necessary in the promotion of cross-pollination in D. pulcherrima. RESULTS Our observations indicated that Doritis pulcherrima is pollinated almost exclusively by Amegilla nigritar (Hymenoptera: Apidae) and possesses pollinia that are deposited on the "occiputs" (cervical membranes) of these insects. All of evidences are indicated that D. pulcherrima is a generalized food-deceptive orchid. Our morphometric measurements of the flowers and pollinators show that the heights of the "occiputs" with un-oriented pollinaria were equal to the distances between stigmas and surfaces of the middle lobes, suggesting that pollinarium reconfiguration is not necessary in Doritis pulcherrima. CONCLUSIONS Our observation and analyses supported the hypothesis that pollinarium reconfiguration is unnecessary in generalized food-deceptive orchids, such as Doritis pulcherrima, for the promotion of cross-pollination. This conclusion was indirectly supported by the abundance of deceptive orchids that do not exhibit pollinarium reconfiguration. There are two mechanisms (i.e. clone-growing characteristics and a long flowering season) that promote fruit sets in the epiphytic food-deceptive orchids in tropical regions.
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Affiliation(s)
- Jin Xiaohua
- State Key Laboratory of Systematic and Evolutionary Botany & Herbarium, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Dezhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ren Zongxin
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiang Xiaoguo
- State Key Laboratory of Systematic and Evolutionary Botany & Herbarium, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Guo YY, Luo YB, Liu ZJ, Wang XQ. Evolution and biogeography of the slipper orchids: Eocene vicariance of the conduplicate genera in the Old and New World Tropics. PLoS One 2012; 7:e38788. [PMID: 22685605 PMCID: PMC3369861 DOI: 10.1371/journal.pone.0038788] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
Intercontinental disjunctions between tropical regions, which harbor two-thirds of the flowering plants, have drawn great interest from biologists and biogeographers. Most previous studies on these distribution patterns focused on woody plants, and paid little attention to herbs. The Orchidaceae is one of the largest families of angiosperms, with a herbaceous habit and a high species diversity in the Tropics. Here we investigate the evolutionary and biogeographical history of the slipper orchids, which represents a monophyletic subfamily (Cypripedioideae) of the orchid family and comprises five genera that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of slipper orchids was reconstructed based on sequence analyses of six maternally inherited chloroplast and two low-copy nuclear genes (LFY and ACO). We found that the genus Cypripedium with a wide distribution in the northern temperate and subtropical zones diverged first, followed by Selenipedium endemic to South America, and finally conduplicate-leaved genera in the Tropics. Mexipedium and Phragmipedium from the neotropics are most closely related, and form a clade sister to Paphiopedilum from tropical Asia. According to molecular clock estimates, the genus Selenipedium originated in Palaeocene, while the most recent common ancestor of conduplicate-leaved slipper orchids could be dated back to the Eocene. Ancestral area reconstruction indicates that vicariance is responsible for the disjunct distribution of conduplicate slipper orchids in palaeotropical and neotropical regions. Our study sheds some light on mechanisms underlying generic and species diversification in the orchid family and tropical disjunctions of herbaceous plant groups. In addition, we suggest that the biogeographical study should sample both regional endemics and their widespread relatives.
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Affiliation(s)
- Yan-Yan Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Zhong-Jian Liu
- The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
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Eum SM, Gale S, Yukawa T, Lee NS. Phylogenetic and conservation status of the endangered terrestrial orchid Nervilia nipponica (Orchidaceae) in Korea. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Xiang XG, Hu H, Wang W, Jin XH. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Mol Ecol Resour 2011; 11:1012-21. [PMID: 21722327 DOI: 10.1111/j.1755-0998.2011.03044.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orchidaceae is one of the largest families of flowering plants. Many species of orchid are endangered, and all species are included in Conventions on International Trade of Endangered Species of Fauna and Flora (CITES) I and II, but it is very difficult to identify orchid species, even those with fertile parts. The genus Holcoglossum (Orchidaceae: Aeridinae) has long been problematic in taxonomy. It consists of both long-evolved and radiated species and is an excellent case to use for testing DNA barcodes for Orchidaceae. We investigated the power of a subset of proposed plant barcoding loci [rbcL, matK, atpF-atpH, psbK-psbI, trnH-psbA and internal transcribed spacer (ITS)] to discriminate between species in this genus. Our results showed that all these DNA regions, except psbK-psbI and atpF-atpH, can be amplified easily from Holcoglossum and sequenced with established primers. The DNA regions matK and ITS had the highest variability. Among the six loci, matK resolved eight of the 12 Holcoglossum species and had the highest discriminatory ability. However, the combination of matK and ITS showed a greater ability to identify species than matK alone. Single or combined DNA markers discriminated between Holcoglossum species distributed in tropical areas effectively, but had less ability to identify radiated species from the temperate Hengduan Mountains of China. In the study, matK proved to be a useful DNA barcode for the genus Holcoglossum; however, complementary DNA regions are still required to accelerate the investigation and preservation of radiated species of orchid.
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Affiliation(s)
- Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Molecular phylogenetics of Hypoxidaceae – Evidence from plastid DNA data and inferences on morphology and biogeography. Mol Phylogenet Evol 2011; 60:122-36. [DOI: 10.1016/j.ympev.2011.02.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 02/02/2011] [Accepted: 02/14/2011] [Indexed: 11/20/2022]
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Stpiczyńska M, Davies KL, Kamińska M. Comparative anatomy of the nectary spur in selected species of Aeridinae (Orchidaceae). ANNALS OF BOTANY 2011; 107:327-45. [PMID: 21183455 PMCID: PMC3043926 DOI: 10.1093/aob/mcq246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS To date, the structure of the nectary spur of Aeridinae has not been studied in detail, and data relating to the nectaries of ornithophilous orchids remain scarce. The present paper compares the structural organization of the floral nectary in a range of Aeridinae species, including both entomophilous and ornithophilous taxa. METHODS Nectary spurs of Ascocentrum ampullaceum (Roxb.) Schltr. var. aurantiacum Pradhan, A. curvifolium (Lindl.) Schltr., A. garayi Christenson, Papilionanthe vandarum (Rchb.f.) Garay, Schoenorchis gemmata (Lindl.) J.J. Sm., Sedirea japonica (Rchb.f.) Garay & H.R. Sweet and Stereochilus dalatensis (Guillaumin) Garay were examined by means of light microscopy, scanning electron microscopy and transmission electron microscopy. KEY RESULTS AND CONCLUSIONS The diverse anatomy of the nectary is described for a range of Aeridinae species. All species of Ascocentrum investigated displayed features characteristic of ornithophilous taxa. They have weakly zygomorphic, scentless, red or orange flowers, display diurnal anthesis, possess cryptic anther caps and produce nectar that is secluded in a relatively massive nectary spur. Unicellular, secretory hairs line the lumen at the middle part of the spur. Generally, however, with the exception of Papilionanthe vandarum, the nectary spurs of all entomophilous species studied here (Schoenorchis gemmata, Sedirea japonica, Stereochilus dalatensis) lack secretory trichomes. Moreover, collenchymatous secretory tissue, present only in the nectary spur of Asiatic Ascocentrum species, closely resembles that found in nectaries of certain Neotropical species that are hummingbird-pollinated and assigned to subtribes Maxillariinae Benth., Laeliinae Benth. and Oncidiinae Benth. This similarity in anatomical organization of the nectary, regardless of geographical distribution and phylogeny, indicates convergence.
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Affiliation(s)
- Małgorzata Stpiczyńska
- University of Life Sciences, ul. Akademicka 15, 20-950 Lublin, Poland
- University of Warsaw, Botanic Garden, Al. Ujazdowskie 4, 00-478 Warszawa, Poland
| | - Kevin L. Davies
- School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
- For correspondence. E-mail
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Haider N, Nabulsi I, Kamary Y. Identification of Orchidaceae species of Northern West of Syria based on chloroplast DNA. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410080065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae). Mol Phylogenet Evol 2010; 55:911-28. [DOI: 10.1016/j.ympev.2009.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/17/2022]
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