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Madrigal Y, Alzate JF, Pabón-Mora N. Evolution of major flowering pathway integrators in Orchidaceae. PLANT REPRODUCTION 2024; 37:85-109. [PMID: 37823912 PMCID: PMC11180029 DOI: 10.1007/s00497-023-00482-7] [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: 05/29/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.
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Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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2
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Xie X, Lin M, Xiao G, Wang Q, Li Z. Identification and Characterization of the AREB/ABF Gene Family in Three Orchid Species and Functional Analysis of DcaABI5 in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:774. [PMID: 38592811 PMCID: PMC10974128 DOI: 10.3390/plants13060774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
AREB/ABF (ABA response element binding) proteins in plants are essential for stress responses, while our understanding of AREB/ABFs from orchid species, important traditional medicinal and ornamental plants, is limited. Here, twelve AREB/ABF genes were identified within three orchids' complete genomes and classified into three groups through phylogenetic analysis, which was further supported with a combined analysis of their conserved motifs and gene structures. The cis-element analysis revealed that hormone response elements as well as light and stress response elements were widely rich in the AREB/ABFs. A prediction analysis of the orchid ABRE/ABF-mediated regulatory network was further constructed through cis-regulatory element (CRE) analysis of their promoter regions. And it revealed that several dominant transcriptional factor (TF) gene families were abundant as potential regulators of these orchid AREB/ABFs. Expression profile analysis using public transcriptomic data suggested that most AREB/ABF genes have distinct tissue-specific expression patterns in orchid plants. Additionally, DcaABI5 as a homolog of ABA INSENSITIVE 5 (ABI5) from Arabidopsis was selected for further analysis. The results showed that transgenic Arabidopsis overexpressing DcaABI5 could rescue the ABA-insensitive phenotype in the mutant abi5. Collectively, these findings will provide valuable information on AREB/ABF genes in orchids.
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Affiliation(s)
- Xi Xie
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.X.); (M.L.); (G.X.); (Q.W.)
| | - Miaoyan Lin
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.X.); (M.L.); (G.X.); (Q.W.)
| | - Gengsheng Xiao
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.X.); (M.L.); (G.X.); (Q.W.)
| | - Qin Wang
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.X.); (M.L.); (G.X.); (Q.W.)
| | - Zhiyong Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
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3
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Zhao X, Li Y, Zhang MM, He X, Ahmad S, Lan S, Liu ZJ. Research advances on the gene regulation of floral development and color in orchids. Gene 2023; 888:147751. [PMID: 37657689 DOI: 10.1016/j.gene.2023.147751] [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: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Valoroso MC, Lucibelli F, Aceto S. Orchid NAC Transcription Factors: A Focused Analysis of CUPULIFORMIS Genes. Genes (Basel) 2022; 13:genes13122293. [PMID: 36553560 PMCID: PMC9777940 DOI: 10.3390/genes13122293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Plant transcription factors are involved in different developmental pathways. NAC transcription factors (No Apical Meristem, Arabidopsis thaliana Activating Factor, Cup-shaped Cotyledon) act in various processes, e.g., plant organ formation, response to stress, and defense mechanisms. In Antirrhinum majus, the NAC transcription factor CUPULIFORMIS (CUP) plays a role in determining organ boundaries and lip formation, and the CUP homologs of Arabidopsis and Petunia are involved in flower organ formation. Orchidaceae is one of the most species-rich families of angiosperms, known for its extraordinary diversification of flower morphology. We conducted a transcriptome and genome-wide analysis of orchid NACs, focusing on the No Apical Meristem (NAM) subfamily and CUP genes. To check whether the CUP homologs could be involved in the perianth formation of orchids, we performed an expression analysis on the flower organs of the orchid Phalaenopsis aphrodite at different developmental stages. The expression patterns of the CUP genes of P. aphrodite suggest their possible role in flower development and symmetry establishment. In addition, as observed in other species, the orchid CUP1 and CUP2 genes seem to be regulated by the microRNA, miR164. Our results represent a preliminary study of NAC transcription factors in orchids to understand the role of these genes during orchid flower formation.
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Affiliation(s)
- Maria Carmen Valoroso
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici, Italy
- Correspondence: (M.C.V.); (S.A.)
| | - Francesca Lucibelli
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
- Correspondence: (M.C.V.); (S.A.)
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5
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Chen YY, Li C, Hsiao YY, Ho SY, Zhang ZB, Liao CC, Lee BR, Lin ST, Wu WL, Wang JS, Zhang D, Liu KW, Liu DK, Zhao XW, Li YY, Ke SJ, Zhou Z, Huang MZ, Wu YS, Peng DH, Lan SR, Chen HH, Liu ZJ, Wu WS, Tsai WC. OrchidBase 5.0: updates of the orchid genome knowledgebase. BMC PLANT BIOLOGY 2022; 22:557. [PMID: 36456919 PMCID: PMC9717476 DOI: 10.1186/s12870-022-03955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.
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Affiliation(s)
- You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chung‐I Li
- Department of Statistics, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Sau-Yee Ho
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhe-Bin Zhang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Chien-Chi Liao
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Bing-Ru Lee
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shao-Ting Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Jeen-Shing Wang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Diyang Zhang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
| | - Ding-Kun Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xue-Wei Zhao
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yuan-Yuan Li
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Shi-Jie Ke
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Zhuang Zhou
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
| | - Ming-Zhong Huang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yong-Shu Wu
- Education Botanical Garden of Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Dong-Hui Peng
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Si-Ren Lan
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Hong-Hwa Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Zhong-Jian Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, 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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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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Jiang M, Zhu Y, Wu Q, Zhang H. Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2872-2879. [PMID: 34532575 PMCID: PMC8439234 DOI: 10.1080/23802359.2021.1972049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD, ψndhG, ψndhK, and ψndhI, are identified as pseudogenes. Another six ndh genes, ndhA, ndhC, ndhE, ndhF, ndhH, and ndhJ, are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii. The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae.
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Affiliation(s)
- Ming Jiang
- College of Life Sciences, Taizhou University, Taizhou, PR China
| | - Yan Zhu
- College of Life Sciences, Taizhou University, Taizhou, PR China
| | - Qian Wu
- College of Life Sciences, Taizhou University, Taizhou, PR China
| | - Huijuan Zhang
- College of Life Sciences, Taizhou University, Taizhou, PR China
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Hsiao YY, Fu CH, Ho SY, Li CI, Chen YY, Wu WL, Wang JS, Zhang DY, Hu WQ, Yu X, Sun WH, Zhou Z, Liu KW, Huang L, Lan SR, Chen HH, Wu WS, Liu ZJ, Tsai WC. OrchidBase 4.0: a database for orchid genomics and molecular biology. BMC PLANT BIOLOGY 2021; 21:371. [PMID: 34384382 PMCID: PMC8359044 DOI: 10.1186/s12870-021-03140-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/11/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. DESCRIPTION Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. CONCLUSIONS OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/.
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Affiliation(s)
- Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Chih-Hsiung Fu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101 Taiwan
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Sau-Yee Ho
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan, 70101 Taiwan
| | - You-Yi Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Wan-Lin Wu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101 Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Jeen-Shing Wang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Di-Yang Zhang
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wen-Qi Hu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xia Yu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wei-Hong Sun
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zhuang Zhou
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
| | - Ke-Wei Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
| | - Laiqiang Huang
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
| | - Si-Ren Lan
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hong-Hwa Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Zhong-Jian Liu
- Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005 China
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055 China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005 China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 70101 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101 Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101 Taiwan
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Kilobase-scale genomic deletion of DOTFL1 in dendrobium orchids. J Genet Genomics 2021; 49:81-84. [PMID: 34426098 DOI: 10.1016/j.jgg.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/22/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
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10
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Lucibelli F, Valoroso MC, Theißen G, Nolden S, Mondragon-Palomino M, Aceto S. Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development. Int J Mol Sci 2021; 22:ijms22137025. [PMID: 34209912 PMCID: PMC8268020 DOI: 10.3390/ijms22137025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 12/13/2022] Open
Abstract
The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene.
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Affiliation(s)
- Francesca Lucibelli
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy; (F.L.); (M.C.V.)
| | - Maria Carmen Valoroso
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy; (F.L.); (M.C.V.)
| | - Günter Theißen
- Matthias Schleiden Institute of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany; (G.T.); (S.N.)
| | - Susanne Nolden
- Matthias Schleiden Institute of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany; (G.T.); (S.N.)
| | - Mariana Mondragon-Palomino
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, 93040 Regensburg, Germany
- Correspondence: (M.M.-P.); (S.A.)
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy; (F.L.); (M.C.V.)
- Correspondence: (M.M.-P.); (S.A.)
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11
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Huang LM, Huang H, Chuang YC, Chen WH, Wang CN, Chen HH. Evolution of Terpene Synthases in Orchidaceae. Int J Mol Sci 2021; 22:6947. [PMID: 34203299 PMCID: PMC8268431 DOI: 10.3390/ijms22136947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the importance of terpenoids, an increasing number of plants are required to investigate the function and evolution of terpene synthases (TPSs) that are the key enzymes in terpenoids biosynthesis. Orchidacea, containing more than 800 genera and 28,000 species, is one of the largest and most diverse families of flowering plants, and is widely distributed. Here, the diversification of the TPSs evolution in Orchidaceae is revealed. A characterization and phylogeny of TPSs from four different species with whole genome sequences is available. Phylogenetic analysis of orchid TPSs indicates these genes are divided into TPS-a, -b, -e/f, and g subfamilies, and their duplicated copies are increased in derived orchid species compared to that in the early divergence orchid, A. shenzhenica. The large increase of both TPS-a and TPS-b copies can probably be attributed to the pro-duction of different volatile compounds for attracting pollinators or generating chemical defenses in derived orchid lineages; while the duplications of TPS-g and TPS-e/f copies occurred in a species-dependent manner.
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Affiliation(s)
- Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Wen-Huei Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Neng Wang
- Department of Life Sciences, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
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12
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Orchid B sister gene PeMADS28 displays conserved function in ovule integument development. Sci Rep 2021; 11:1205. [PMID: 33441740 PMCID: PMC7806631 DOI: 10.1038/s41598-020-79877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
The ovules and egg cells are well developed to be fertilized at anthesis in many flowering plants. However, ovule development is triggered by pollination in most orchids. In this study, we characterized the function of a Bsister gene, named PeMADS28, isolated from Phalaenopsis equestris, the genome-sequenced orchid. Spatial and temporal expression analysis showed PeMADS28 predominantly expressed in ovules between 32 and 48 days after pollination, which synchronizes with integument development. Subcellular localization and protein–protein interaction analyses revealed that PeMADS28 could form a homodimer as well as heterodimers with D-class and E-class MADS-box proteins. In addition, ectopic expression of PeMADS28 in Arabidopsis thaliana induced small curled rosette leaves, short silique length and few seeds, similar to that with overexpression of other species’ Bsister genes in Arabidopsis. Furthermore, complementation test revealed that PeMADS28 could rescue the phenotype of the ABS/TT16 mutant. Together, these results indicate the conserved function of BsisterPeMADS28 associated with ovule integument development in orchid.
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Liang CY, Rengasamy KP, Huang LM, Hsu CC, Jeng MF, Chen WH, Chen HH. Assessment of violet-blue color formation in Phalaenopsis orchids. BMC PLANT BIOLOGY 2020; 20:212. [PMID: 32397954 PMCID: PMC7218627 DOI: 10.1186/s12870-020-02402-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/22/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Phalaenopsis represents an important cash crop worldwide. Abundant flower colors observed in Phalaenopsis orchids range from red-purple, purple, purple-violet, violet, and violet-blue. However, violet-blue orchids are less bred than are those of other colors. Anthocyanin, vacuolar pH and metal ions are three major factors influencing flower color. This study aimed to identify the factors causing the violet-blue color in Phalaenopsis flowers and to analyze whether delphinidin accumulation and blue pigmentation formation can be achieved by transient overexpression of heterologous F3'5'H in Phalaenopsis. RESULTS Cyanidin-based anthocyanin was highly accumulated in Phalaenopsis flowers with red-purple, purple, purple-violet, and violet to violet-blue color, but no true-blue color and no delphinidin was detected. Concomitantly, the expression of PeF3'H (Phalaenopsis equestrsis) was high, but that of PhF3'5'H (Phalaenopsis hybrid) was low or absent in various-colored Phalaenopsis flowers. Transient overexpression of DgF3'5'H (Delphinium grandiflorum) and PeMYB2 in a white Phalaenopsis cultivar resulted a 53.6% delphinidin accumulation and a novel blue color formation. In contrast, transient overexpression of both PhF3'5'H and PeMYB2 did not lead to delphinidin accumulation. Sequence analysis showed that the substrate recognition site 6 (SRS6) of PhF3'5'H was consistently different from DgF3'5'Hs at positions 5, 8 and 10. Prediction of molecular docking of the substrates showed a contrary binding direction of aromatic rings (B-ring) with the SRS6 domain of DgF3'5'H and PhF3'5'H. In addition, the pH values of violet-blue and purple Phalaenopsis flowers ranged from 5.33 to 5.54 and 4.77 to 5.04, respectively. Furthermore, the molar ratio of metal ions (including Al3+, Ca2+ and Fe3+) to anthocyanin in violet-blue color Phalaenopsis was 190-, 49-, and 51-fold higher, respectively, than those in purple-color Phalaenopsis. CONCLUSION Cyanidin-based anthocyanin was detected in violet-blue color Phalaenopsis and was concomitant with a high pH value and high molar ratio of Al3+, Ca2+ and Fe3+ to anthocyanin content. Enhanced expression of delphinidin is needed to produce true-blue Phalaenopsis.
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Affiliation(s)
- Che-Yu Liang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | | | - Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Mei-Fen Jeng
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wen-Huei Chen
- Department of Life 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, Tainan, 701, Taiwan.
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
- , Nantou City, Taiwan.
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Hsieh KT, Liu SH, Wang IW, Chen LJ. Phalaenopsis orchid miniaturization by overexpression of OsGA2ox6, a rice GA2-oxidase gene. BOTANICAL STUDIES 2020; 61:10. [PMID: 32253516 PMCID: PMC7136379 DOI: 10.1186/s40529-020-00288-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/28/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Phalaenopsis orchids are one of the most common potted orchids sold worldwide. Most Phalaenopsis cultivars have long inflorescences that cause shipping problems and increase handling costs. Miniaturization of Phalaenopsis orchids not only reduces overall production costs but also can expand the appeal of the orchids to a different group of consumers who prefer to keep flowers on desks or tabletops. Although some miniature Phalaenopsis plants can be obtained via hybridization or mutation, they are unpredictable and limited in variety. We therefore used the transgenic approach of overexpressing gibberellin 2-oxidase 6 (OsGA2ox6), a rice GA deactivation gene, to investigate its functional effect in miniaturizing Phalaenopsis and to create a stable miniaturization platform to facilitate a supply for the potential demands of the miniature flower market. RESULTS A commercial moth orchid, Phalaenopsis Sogo Yukidian 'SPM313', was transformed with the plasmid vector Ubi:OsGA2ox6 and successfully overexpressed the OsGA2ox6 gene in planta. The transgenic lines displayed darker-green, shorter, and wider leaves, thicker roots and much shorter flower spikes (10 cm vs 33 cm) than the nontransgenic line with a normal flower size and blooming ability and are therefore an ideal miniaturized form of Phalaenopsis orchids. CONCLUSIONS We demonstrated that the ectopic expression of OsGA2ox6 can miniaturize Phalaenopsis Sogo Yukidian 'SPM313' while preserving its blooming ability, providing an alternative, useful method for miniaturizing Phalaenopsis species. This miniaturization by a transgenic approach can be further expanded by using GA2ox genes from different plant species or different gene variants, thereby expanding the technical platform for miniaturizing Phalaenopsis species to meet the potential demands of the miniature Phalaenopsis flower market.
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Affiliation(s)
- Kun-Ting Hsieh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Su-Hui Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - I-Wen Wang
- Division of Biotechnology, Taiwan Agriculture Research Institute, Taichung, 41362 Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227 Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
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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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Lai PH, Huang LM, Pan ZJ, Jane WN, Chung MC, Chen WH, Chen HH. PeERF1, a SHINE-Like Transcription Factor, Is Involved in Nanoridge Development on Lip Epidermis of Phalaenopsis Flowers. FRONTIERS IN PLANT SCIENCE 2020; 10:1709. [PMID: 32082333 PMCID: PMC7002429 DOI: 10.3389/fpls.2019.01709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Phalaenopsis orchids have a spectacular floral morphology with a highly evolved lip that offers a landing platform for pollinators. The typical morphological orchid lip features are essential for the special pollination mechanism of Phalaenopsis flowers. Previously, we found that in the lip, a member of the AP2/EREBP protein family was highly expressed. Here, we further confirmed its high expression and characterized its function during lip development. Phylogenetic analysis showed that AP2/EREBP belongs to the Va2 subgroup of ERF transcription factors. We named it PeERF1. We found that PeERF1 was only expressed at stage 5, as flowers opened. This coincided with both thickening of the cuticle and development of nanoridges. We performed knockdown expression of PeERF1 using CymMV-based virus-induced gene silencing in either the AP2 conserved domain, producing PeERF1_AP2-silenced plants, or the SHN specific domain, producing PeERF1_SHN-silenced plants. Using cryo-SEM, we found that the number of nanoridges was reduced only in the PeERF1_AP2-silenced group. This change was found on both the abaxial and adaxial surfaces of the central lip lobe. Expression of PeERF1 was reduced significantly in PeERF1_AP2-silenced plants. In cutin biosynthesis genes, expression of both PeCYP86A2 and PeDCR was significantly decreased in both groups. The expression of PeCYP77A4 was reduced significantly only in the PeERF1_AP2-silenced plants. Although PeGPAT expression was reduced in both silenced plants, but to a lesser degree. The expression of PeERF1 was significantly reduced in the petal-like lip of a big-lip variant. PeCYP77A4 and PeGPAT in the lip were also reduced, but PeDCR was not. Furthermore, heterologous overexpression of PeERF1 in the genus Arabidopsis produced leaves that were shiny on the adaxial surface. Taken together, our results show that in Phalaenopsis orchids PeERF1 plays an important role in formation of nanoridges during lip epidermis development.
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Affiliation(s)
- Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Zhao-Jun Pan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
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Nakatsuka T, Suzuki T, Harada K, Kobayashi Y, Dohra H, Ohno H. Floral organ- and temperature-dependent regulation of anthocyanin biosynthesis in Cymbidium hybrid flowers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110173. [PMID: 31481204 DOI: 10.1016/j.plantsci.2019.110173] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/17/2019] [Accepted: 06/20/2019] [Indexed: 05/24/2023]
Abstract
Anthocyanins are responsible for red, purple, and pink pigmentation of flowers in Cymbidium hybrids. Although anthocyanin content in all floral organs increases with flower development, they increase markedly in the tepals compared with the labella or columns. Using next-generation sequencing technology, we identified three anthocyanin biosynthesis regulatory genes, CyMYB1, CybHLH1, and CybHLH2, from Cymbidium 'Mystique'. Yeast two-hybrid analysis showed that the CyMYB1 protein can form a heterodimer with either CybHLH1 or CybHLH2. In the tepals, the expression level of CyMYB1 increased as the flower developed, whereas the high expression level of CyMYB1 was detected at the early flower developmental stages in the labella and columns, remaining constant until increasing at the late developmental stage. These expression profiles of CyMYB1 positively correlated with the profiles of anthocyanin accumulation in the tepals. When Cymbidium Sazanami 'Champion' was grown at 30 °C/25 °C, reduced anthocyanin levels were observed, specifically in the tepals, compared with those in flowers grown at 20 °C/15 °C. The transcription of CyMYB1 in the tepals was suppressed at high temperatures, and the expressions of CyDFR and CyANS were also synchronously suppressed. This study revealed that CyMYB1 activates the transcription of CyDFR and CyANS and regulates the temporal- and temperature-dependent anthocyanin accumulation in Cymbidium tepals.
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Affiliation(s)
- Takashi Nakatsuka
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan; College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
| | - Tomohiro Suzuki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan; Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8508, Japan
| | - Kenji Harada
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Yuki Kobayashi
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hajime Ohno
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan; College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan
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Madrigal Y, Alzate JF, González F, Pabón-Mora N. Evolution of RADIALIS and DIVARICATA gene lineages in flowering plants with an expanded sampling in non-core eudicots. AMERICAN JOURNAL OF BOTANY 2019; 106:334-351. [PMID: 30845367 DOI: 10.1002/ajb2.1243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/07/2018] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Bilateral symmetry in core eudicot flowers is established by the differential expression of CYCLOIDEA (CYC), DICHOTOMA (DICH), and RADIALIS (RAD), which are restricted to the dorsal portion of the flower, and DIVARICATA (DIV), restricted to the ventral and lateral petals. Little is known regarding the evolution of these gene lineages in non-core eudicots, and there are no reports on gene expression that can be used to assess whether the network predates the diversification of core eudicots. METHODS Homologs of the RAD and DIV lineages were isolated from available genomes and transcriptomes, including those of three selected non-core eudicot species, the magnoliid Aristolochia fimbriata and the monocots Cattleya trianae and Hypoxis decumbens. Phylogenetic analyses for each gene lineage were performed. RT-PCR was used to evaluate the expression and putative contribution to floral symmetry in dissected floral organs of the selected species. KEY RESULTS RAD-like genes have undergone at least two duplication events before eudicot diversification, three before monocots and at least four in Orchidaceae. DIV-like genes also duplicated twice before eudicot diversification and underwent independent duplications specific to Orchidaceae. RAD-like and DIV-like genes have differential dorsiventral expression only in C. trianae, which contrasts with the homogeneous expression in the perianth of A. fimbriata. CONCLUSIONS Our results point to a common genetic regulatory network for floral symmetry in monocots and core eudicots, while alternative genetic mechanisms are likely driving the bilateral perianth symmetry in the early-diverging angiosperm Aristolochia.
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Affiliation(s)
- Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, AA 1226, Cl. 67 No. 53-108, Medellín, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica, SIU, Facultad de Medicina, Universidad de Antioquia, Cl. 70 No. 52-21, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, AA. 7495, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, AA 1226, Cl. 67 No. 53-108, Medellín, Colombia
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19
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Hsu CC, Lai PH, Chen TC, Tsai WC, Hsu JL, Hsiao YY, Wu WL, Tsai CH, Chen WH, Chen HH. PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids. BMC Genomics 2019; 20:25. [PMID: 30626325 PMCID: PMC6327408 DOI: 10.1186/s12864-018-5420-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/27/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation. RESULTS We isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced. CONCLUSION A PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tien-Chih Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
| | - Jui-Lin Hsu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Luan Wu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
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Teo ZWN, Zhou W, Shen L. Dissecting the Function of MADS-Box Transcription Factors in Orchid Reproductive Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1474. [PMID: 31803211 PMCID: PMC6872546 DOI: 10.3389/fpls.2019.01474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/23/2019] [Indexed: 05/20/2023]
Abstract
The orchid family (Orchidaceae) represents the second largest angiosperm family, having over 900 genera and 27,000 species in almost all over the world. Orchids have evolved a myriad of intriguing ways in order to survive extreme weather conditions, acquire nutrients, and attract pollinators for reproduction. The family of MADS-box transcriptional factors have been shown to be involved in the control of many developmental processes and responses to environmental stresses in eukaryotes. Several findings in different orchid species have elucidated that MADS-box genes play critical roles in the orchid growth and development. An in-depth understanding of their ecological adaptation will help to generate more interest among breeders and produce novel varieties for the floriculture industry. In this review, we summarize recent findings of MADS-box transcription factors in regulating various growth and developmental processes in orchids, in particular, the floral transition and floral patterning. We further discuss the prospects for the future directions in light of new genome resources and gene editing technologies that could be applied in orchid research and breeding.
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Affiliation(s)
- Zhi Wei Norman Teo
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Wei Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- *Correspondence: Lisha Shen,
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21
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Kuo YT, Chao YT, Chen WC, Shih MC, Chang SB. Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. ANNALS OF BOTANY 2019; 123:69-77. [PMID: 30113635 PMCID: PMC6344096 DOI: 10.1093/aob/mcy136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/22/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Orchidaceae is a large plant family, and its extraordinary adaptations may have guaranteed its evolutionary success. Flavonoids are a group of secondary metabolites that mediate plant acclimation to challenge environments. Chalcone synthase (CHS) catalyses the initial step in the flavonoid biosynthetic pathway. This is the first chromosome-level investigation of the CHS gene family in Phalaenopsis aphrodite and was conducted to elucidate if divergence of this gene family is associated with chromosome evolution. METHODS Complete CHS genes were identified from our whole-genome sequencing data sets and their gene expression profiles were obtained from our transcriptomic data sets. Fluorescence in situ hybridization (FISH) was conducted to position five CHS genes to high-resolution pachytene chromosomes. KEY RESULTS The five Phalaenopsis CHS genes can be classified into three groups, PaCHS1, PaCHS2 and the tandemly arrayed three-gene cluster, which diverged earlier than those of the orchid genera and species. Additionally, pachytene chromosome-based FISH mapping showed that the three groups of CHS genes are localized on three distinct chromosomes. Moreover, an expression analysis of RNA sequencing revealed that the five CHS genes had highly differentiated expression patterns and its expression pattern-based clustering showed high correlations between sequence divergences and chromosomal localizations of the CHS gene family in P. aphrodite. CONCLUSIONS Based on their phylogenetic relationships, expression clustering analysis and chromosomal distributions of the five paralogous PaCHS genes, we proposed that expansion of this gene family in P. aphrodite occurred through segmental duplications, followed by tandem duplications. These findings provide information for further studies of CHS functions and regulations, and shed light on the divergence of an important gene family in orchids.
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Affiliation(s)
- Yi-Tzu Kuo
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- For correspondence. E-mail:
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22
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Ping CY, Chen FC, Cheng TC, Lin HL, Lin TS, Yang WJ, Lee YI. Expression Profiles of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxylase Kinase Genes in Phalaenopsis, Implications for Regulating the Performance of Crassulacean Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2018; 9:1587. [PMID: 30425727 PMCID: PMC6218735 DOI: 10.3389/fpls.2018.01587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/12/2018] [Indexed: 05/26/2023]
Abstract
Phalaenopsis is one of the most important potted plants in the ornamental market of the world. Previous reports implied that crassulacean acid metabolism (CAM) orchids at their young seedling stages might perform C3 or weak CAM photosynthetic pathways, but the detailed molecular evidence is still lacking. In this study, we used a key species in white Phalaenopsis breeding line, Phalaenopsis aphrodite subsp. formosana, to study the ontogenetical changes of CAM performance in Phalaenopsis. Based on the investigations of rhythms of day/night CO2 exchange, malate contents and phosphoenolpyruvate carboxylase (PEPC) activities, it is suggested that a progressive shift from C3 to CAM occurred as the protocorms differentiated the first leaf. To understand the role of phosphoenolpyruvate carboxylase kinase (PEPC kinase) in relation to its target PEPC in CAM performance in Phalaenopsis, the expression profiles of the genes encoding PEPC (PPC) and PEPC kinase (PPCK) were measured in different developmental stages. In Phalaenopsis, two PPC isogenes were constitutively expressed over a 24-h cycle similar to the housekeeping genes in all stages, whereas the significant day/night difference in PaPPCK expression corresponds to the day/night fluctuations in PEPC activity and malate level. These results suggest that the PaPPCK gene product is most likely involved in regulation of CAM performance in different developmental stages of Phalaenopsis seedlings.
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Affiliation(s)
- Chia-Yun Ping
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Teen-Chi Cheng
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Huey-Ling Lin
- Department of Horticulture, National Chung Hsing University, Taichung, Taiwan
| | - Tzong-Shyan Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Wen-Ju Yang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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23
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Liu D, Palla KJ, Hu R, Moseley RC, Mendoza C, Chen M, Abraham PE, Labbé JL, Kalluri UC, Tschaplinski TJ, Cushman JC, Borland AM, Tuskan GA, Yang X. Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:394-401. [PMID: 30080627 DOI: 10.1016/j.plantsci.2018.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 05/24/2023]
Abstract
Due to public concerns about the decreasing supply of blue water and increasing heat and drought stress on plant growth caused by urbanization, increasing human population and climate change, interest in crassulacean acid metabolism (CAM), a specialized type of photosynthesis enhancing water-use efficiency (WUE) and drought tolerance, has increased markedly. Significant progress has been achieved in both basic and applied research in CAM plants since the beginning of this century. Here we provide a brief overview of the current status of CAM research, and discuss future needs and opportunities in a wide range of areas including systems biology, synthetic biology, and utilization of CAM crops for human benefit, with a focus on the following aspects: 1) application of genome-editing technology and high-throughput phenotyping to functional genomics research in model CAM species and genetic improvement of CAM crops, 2) challenges for multi-scale metabolic modeling of CAM systems, 3) opportunities and new strategies for CAM pathway engineering to enhance WUE and drought tolerance in C3 (and C4) photosynthesis crops, 4) potential of CAM species as resources for food, feed, natural products, pharmaceuticals and biofuels, and 5) development of CAM crops for ecological and aesthetic benefits.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Robert C Moseley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - Christopher Mendoza
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Mei Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Udaya C Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA.
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Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:11640. [PMID: 30076357 PMCID: PMC6076244 DOI: 10.1038/s41598-018-30147-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/24/2018] [Indexed: 11/15/2022] Open
Abstract
Deceptive pollination is key to the species richness of Orchidaceae. However, the genetic basis of species diversification is still under study. Section Trigonopedia is a monophyletic clade of genus Cypripedium distributed in the southwest of China. The species of this section are pollinated by different flies. Pollinator differentiation makes section Trigonopedia an ideal group for studying the genetic basis underlying species diversification. Here, we sequenced the transcriptomes of eight species of the genus Cypripedium, including six co-flowering species of section Trigonopedia and two species outside this section as an outgroup. We reconstructed the phylogeny of the section with the combined 1572 single-copy genes extracted from the eight species and produced a highly resolved tree of the section. Furthermore, we combined substitution rate estimation and differential expression analysis to identify candidate genes, including genes related to floral scent synthesis and environmental adaptation, involved in species differentiation. Field investigations showed that these species have adapted to different habitats. We propose that the species diversification in this section is initiated by floral scent differentiation, followed by habitat differentiation, finally leading to speciation. This study sheds novel light on the diversification of closely related orchid species in the Qinghai-Tibetan region.
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25
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Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA. SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database (Oxford) 2018; 2018:4995113. [PMID: 29762652 PMCID: PMC5946812 DOI: 10.1093/database/bay035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/20/2023]
Abstract
Database URL https://solgenomics.net/tools/solcyc/.
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Affiliation(s)
- Hartmut Foerster
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 220 Ag Quad Lane, Blacksburg, VA 24061, USA
| | - James N D Battey
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
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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: 17] [Impact Index Per Article: 2.4] [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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Niu Z, Xue Q, Zhu S, Sun J, Liu W, Ding X. The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots. FRONTIERS IN PLANT SCIENCE 2017; 8:715. [PMID: 28515737 PMCID: PMC5413554 DOI: 10.3389/fpls.2017.00715] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/18/2017] [Indexed: 05/20/2023]
Abstract
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5'trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic.
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Affiliation(s)
| | | | | | | | | | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal UniversityNanjing, China
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Madrigal Y, Alzate JF, Pabón-Mora N. Evolution and Expression Patterns of TCP Genes in Asparagales. FRONTIERS IN PLANT SCIENCE 2017; 8:9. [PMID: 28144250 PMCID: PMC5239819 DOI: 10.3389/fpls.2017.00009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/03/2017] [Indexed: 05/09/2023]
Abstract
CYCLOIDEA-like genes are involved in the symmetry gene network, limiting cell proliferation in the dorsal regions of bilateral flowers in core eudicots. CYC-like and closely related TCP genes (acronym for TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR) have been poorly studied in Asparagales, the largest order of monocots that includes both bilateral flowers in Orchidaceae (ca. 25.000 spp) and radially symmetrical flowers in Hypoxidaceae (ca. 200 spp). With the aim of assessing TCP gene evolution in the Asparagales, we isolated TCP-like genes from publicly available databases and our own transcriptomes of Cattleya trianae (Orchidaceae) and Hypoxis decumbens (Hypoxidaceae). Our matrix contains 452 sequences representing the three major clades of TCP genes. Besides the previously identified CYC specific core eudicot duplications, our ML phylogenetic analyses recovered an early CIN-like duplication predating all angiosperms, two CIN-like Asparagales-specific duplications and a duplication prior to the diversification of Orchidoideae and Epidendroideae. In addition, we provide evidence of at least three duplications of PCF-like genes in Asparagales. While CIN-like and PCF-like genes have multiplied in Asparagales, likely enhancing the genetic network for cell proliferation, CYC-like genes remain as single, shorter copies with low expression. Homogeneous expression of CYC-like genes in the labellum as well as the lateral petals suggests little contribution to the bilateral perianth in C. trianae. CIN-like and PCF-like gene expression suggests conserved roles in cell proliferation in leaves, sepals and petals, carpels, ovules and fruits in Asparagales by comparison with previously reported functions in core eudicots and monocots. This is the first large scale analysis of TCP-like genes in Asparagales that will serve as a platform for in-depth functional studies in emerging model monocots.
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Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Facultad de Medicina, Universidad de AntioquiaMedellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
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Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0-A Transcriptomics Resource for the Orchid Family. PLANT & CELL PHYSIOLOGY 2017; 58:e9. [PMID: 28111366 DOI: 10.1093/pcp/pcw220] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/01/2016] [Indexed: 05/18/2023]
Abstract
Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2.0 has been built with a new database system to store the annotations of 510,947 protein-coding genes and 161,826 noncoding transcripts, covering 18 orchid species belonging to 12 genera in five subfamilies of Orchidaceae. We have improved the N50 size of protein-coding genes, provided new functional annotations (including protein-coding gene annotations, protein domain/family information, pathways analysis, Gene Ontology term assignments, orthologous genes across orchid species, cross-links to the database of model species, and miRNA information), and improved the user interface with better website performance. We also provide new database functionalities for database searching and sequence retrieval. Moreover, the Orchidstra 2.0 database incorporates detailed RNA-Seq gene expression data from various tissues and developmental stages in different orchid species. The database will be useful for gene prediction and gene family studies, and for exploring gene expression in orchid species. The Orchidstra 2.0 database is freely accessible at http://orchidstra2.abrc.sinica.edu.tw.
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Affiliation(s)
- Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shao-Hua Yen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jen-Hau Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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Niu SC, Xu Q, Zhang GQ, Zhang YQ, Tsai WC, Hsu JL, Liang CK, Luo YB, Liu ZJ. De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. Sci Data 2016; 3:160083. [PMID: 27673730 PMCID: PMC5037975 DOI: 10.1038/sdata.2016.83] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/24/2016] [Indexed: 01/19/2023] Open
Abstract
Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search.
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Affiliation(s)
- Shan-Ce Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China
| | - 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
| | - Jui-Ling Hsu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Chieh-Kai Liang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen 518114, China.,The Centre for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510640, China.,College of Arts, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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31
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Huang JZ, Lin CP, Cheng TC, Huang YW, Tsai YJ, Cheng SY, Chen YW, Lee CP, Chung WC, Chang BCH, Chin SW, Lee CY, Chen FC. The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation. PeerJ 2016; 4:e2017. [PMID: 27190718 PMCID: PMC4868593 DOI: 10.7717/peerj.2017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/17/2016] [Indexed: 01/28/2023] Open
Abstract
The Phalaenopsis orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of PhAGL6b in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing PhAGL6b leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.
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Affiliation(s)
- Jian-Zhi Huang
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan.,Department of Biotechnology, School of Health Technology, Ming Chuan University, Gui Shan District, Taoyuan, Taiwan
| | - Ting-Chi Cheng
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Ya-Wen Huang
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yi-Jung Tsai
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shu-Yun Cheng
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yi-Wen Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chueh-Pai Lee
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | - Wan-Chia Chung
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | - Bill Chia-Han Chang
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan.,Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Shih-Wen Chin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chen-Yu Lee
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
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32
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Sharma SK, Mukai Y. Chromosome research in orchids: current status and future prospects with special emphasis from molecular and epigenetic perspective. THE NUCLEUS 2016. [DOI: 10.1007/s13237-015-0152-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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33
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Deng H, Zhang LS, Zhang GQ, Zheng BQ, Liu ZJ, Wang Y. Evolutionary history of PEPC genes in green plants: Implications for the evolution of CAM in orchids. Mol Phylogenet Evol 2016; 94:559-564. [DOI: 10.1016/j.ympev.2015.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 11/15/2022]
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34
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Molecular cytogenetic use of BAC clones in Neofinetia falcata and Rhynchostylis coelestis. THE NUCLEUS 2015. [DOI: 10.1007/s13237-015-0147-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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35
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De Paolo S, Gaudio L, Aceto S. Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica. Sci Rep 2015; 5:16265. [PMID: 26531864 PMCID: PMC4632031 DOI: 10.1038/srep16265] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/13/2015] [Indexed: 11/09/2022] Open
Abstract
TCP proteins are plant-specific transcription factors involved in many different processes. Because of their involvement in a large number of developmental pathways, their roles have been investigated in various plant species. However, there are almost no studies of this transcription factor family in orchids. Based on the available transcriptome of the inflorescence of the orchid Orchis italica, in the present study we identified 12 transcripts encoding TCP proteins. The phylogenetic analysis showed that they belong to different TCP classes (I and II) and groups (PCF, CIN and CYC/TB1), and that they display a number of conserved motifs when compared with the TCPs of Arabidopsis and Oryza. The presence of a specific cleavage site for the microRNA miRNA319, an important post-transcriptional regulator of several TCP genes in other species, was demonstrated for one transcript of O. italica, and the analysis of the expression pattern of the TCP transcripts in different inflorescence organs and in leaf tissue suggests that some TCP transcripts of O. italica exert their role only in specific tissues, while others may play multiple roles in different tissues. In addition, the evolutionary analysis showed a general purifying selection acting on the coding region of these transcripts.
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Affiliation(s)
- Sofia De Paolo
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Luciano Gaudio
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, Napoli, Italy
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36
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Hsu CC, Chen YY, Tsai WC, Chen WH, Chen HH. Three R2R3-MYB transcription factors regulate distinct floral pigmentation patterning in Phalaenopsis spp. PLANT PHYSIOLOGY 2015; 168:175-91. [PMID: 25739699 PMCID: PMC4424010 DOI: 10.1104/pp.114.254599] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/27/2015] [Indexed: 05/19/2023]
Abstract
Orchidaceae are well known for their fascinating floral morphologic features, specialized pollination, and distinctive ecological strategies. With their long-lasting flowers of various colors and pigmentation patterning, Phalaenopsis spp. have become important ornamental plants worldwide. In this study, we identified three R2R3-MYB transcription factors PeMYB2, PeMYB11, and PeMYB12. Their expression profiles were concomitant with red color formation in Phalaenopsis spp. flowers. Transient assay of overexpression of three PeMYBs verified that PeMYB2 resulted in anthocyanin accumulation, and these PeMYBs could activate the expression of three downstream structural genes Phalaenopsis spp. Flavanone 3-hydroxylase5, Phalaenopsis spp. Dihydroflavonol 4-reductase1, and Phalaenopsis spp. Anthocyanidin synthase3. In addition, these three PeMYBs participated in the distinct pigmentation patterning in a single flower, which was revealed by virus-induced gene silencing. In the sepals/petals, silencing of PeMYB2, PeMYB11, and PeMYB12 resulted in the loss of the full-red pigmentation, red spots, and venation patterns, respectively. Moreover, different pigmentation patterning was regulated by PeMYBs in the sepals/petals and lip. PeMYB11 was responsive to the red spots in the callus of the lip, and PeMYB12 participated in the full pigmentation in the central lobe of the lip. The differential pigmentation patterning was validated by RNA in situ hybridization. Additional assessment was performed in six Phalaenopsis spp. cultivars with different color patterns. The combined expression of these three PeMYBs in different ratios leads to a wealth of complicated floral pigmentation patterning in Phalaenopsis spp.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Chieh Tsai
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Huei Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
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37
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Lin CS, Chen JJW, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GKS, Albert VA, Chou ML, Chen CY, Shih MC. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Sci Rep 2015; 5:9040. [PMID: 25761566 PMCID: PMC4356964 DOI: 10.1038/srep09040] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 02/16/2015] [Indexed: 11/22/2022] Open
Abstract
The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.
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Affiliation(s)
- Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ming-Tsair Chan
- 1] Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan [2] Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan
| | - Henry Daniell
- Departments of Biochemistry and Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - De-Chih Liao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Fu-Huei Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Sheng-Yi Lin
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Chen-Fu Liao
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gane Ka-Shu Wong
- 1] Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada [2] Department of Medicine, University of Alberta, Edmonton AB, Canada [3] BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Ming-Lun Chou
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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38
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Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ. The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 2014; 47:65-72. [PMID: 25420146 DOI: 10.1038/ng.3149] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/29/2014] [Indexed: 12/21/2022]
Abstract
Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.
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Affiliation(s)
- Jing Cai
- 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Kevin Vanneste
- 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sebastian Proost
- 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ke-Wei Liu
- 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Ying He
- 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Qing Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | - Yu-Yun Hsiao
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Zhao-Jun Pan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ping Yang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Chin Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Anne Dievart
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France
| | - Jean-Francois Dufayard
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | | | - Rong Du
- State Forestry Administration, Beijing, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yong-Yu Su
- College of Forestry, South China Agriculture University, Guangzhou, China
| | - Gao-Chang Xie
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Li-Qiang Li
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Lai-Qiang Huang
- 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China. [4] College of Forestry, South China Agriculture University, Guangzhou, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Hwa Chen
- 1] Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. [2] Orchid Research Center, National Cheng Kung University, Tainan, Taiwan
| | - Yves Van de Peer
- 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. [3] Department of Genetics, Genomics Research Institute, Pretoria, South Africa
| | - Zhong-Jian Liu
- 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] College of Forestry, South China Agriculture University, Guangzhou, China
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39
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Peng PH, Lin CH, Tsai HW, Lin TY. Cold response in Phalaenopsis aphrodite and characterization of PaCBF1 and PaICE1. PLANT & CELL PHYSIOLOGY 2014; 55:1623-35. [PMID: 24974386 DOI: 10.1093/pcp/pcu093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Phalaenopsis is a winter-blooming orchid genus commonly cultivated in tropical Asian countries. Because orchids are one of the most economically important flower crops in Taiwan, it is crucial to understand their response to cold and other abiotic stresses. The present study focused on gene regulation of P. aphrodite in response to abiotic stress, mainly cold. Our results demonstrate that P. aphrodite is sensitive to low temperatures, especially in its reproductive stage. We found that after exposure to 4°C, plants in the vegetative stage maintained better membrane integrity and photosynthetic capacity than in the flowering stage. At the molecular level, C-repeat binding factor1 (PaCBF1) and its putative target gene dehydrin1 (PaDHN1) mRNAs were induced by cold, whereas inducer of CBF expression1 (PaICE1) mRNA was constitutively expressed. PaICE1 transactivated MYC motifs in the PaCBF1 promoter, indicating that up-regulation of PaCBF1 may be mediated by the binding of PaICE1 to MYC motifs. Overexpression of PaCBF1 in transgenic Arabidopsis induced AtCOR6.6 and RD29a without cold stimulus and maintained better membrane integrity after cold stress. Herein, we present evidence that cold induction of PaCBF1 transcripts in P. aphrodite may be transactivated by PaICE1 and consequently protect plants from cold damage through up-regulation of cold-regulated (COR) genes, such as DHN. To our knowledge, this study is the first report of the isolation and characterization of CBF, DHN and ICE genes in the Orchidaceae family.
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Affiliation(s)
- Po-Hsin Peng
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Chia-Hui Lin
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Hui-Wen Tsai
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Tsai-Yun Lin
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
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40
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Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC. Engineering crassulacean acid metabolism to improve water-use efficiency. TRENDS IN PLANT SCIENCE 2014; 19:327-38. [PMID: 24559590 PMCID: PMC4065858 DOI: 10.1016/j.tplants.2014.01.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 01/01/2014] [Accepted: 01/13/2014] [Indexed: 05/19/2023]
Abstract
Climatic extremes threaten agricultural sustainability worldwide. One approach to increase plant water-use efficiency (WUE) is to introduce crassulacean acid metabolism (CAM) into C3 crops. Such a task requires comprehensive systems-level understanding of the enzymatic and regulatory pathways underpinning this temporal CO2 pump. Here we review the progress that has been made in achieving this goal. Given that CAM arose through multiple independent evolutionary origins, comparative transcriptomics and genomics of taxonomically diverse CAM species are being used to define the genetic 'parts list' required to operate the core CAM functional modules of nocturnal carboxylation, diurnal decarboxylation, and inverse stomatal regulation. Engineered CAM offers the potential to sustain plant productivity for food, feed, fiber, and biofuel production in hotter and drier climates.
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Affiliation(s)
- Anne M Borland
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - Karen A Schlauch
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | | | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA.
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Fukami-Kobayashi K, Nakamura Y, Tamura T, Kobayashi M. SABRE2: A Database Connecting Plant EST/Full-Length cDNA Clones with Arabidopsis Information. ACTA ACUST UNITED AC 2014; 55:e5. [DOI: 10.1093/pcp/pct177] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Tsai WC, Pan ZJ, Su YY, Liu ZJ. New insight into the regulation of floral morphogenesis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 311:157-82. [PMID: 24952917 DOI: 10.1016/b978-0-12-800179-0.00003-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The beauty and complexity of flowers have held the fascination of scientists for centuries, from Linnaeus, to Goethe, to Darwin, through to the present. During the past decade, enormous progress has been made in understanding the molecular regulation of flower morphogenesis. It seems likely that there are both highly conserved aspects to flower development in addition to significant differences in developmental patterning that can contribute to the unique morphologies of different species. Furthermore, floral development is attractive in that several key genes regulating fundamental processes have been identified. Crucial functional studies of floral organ identity genes in diverse taxa are allowing the real insight into the conservation of gene function, while findings on the genetic control of organ elaboration open up new avenues for investigation. These fundamentals of floral organ differentiation and growth are therefore an ideal subject for comparative analyses of flower development, which will lead to a better understanding of molecular mechanisms that control flower morphogenesis.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan; Orchid Research Center, National Cheng Kung University, Tainan, Taiwan; Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
| | - Zhao-Jun Pan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yong-Yu Su
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, China; The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & 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.
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Lin HY, Chen JC, Wei MJ, Lien YC, Li HH, Ko SS, Liu ZH, Fang SC. Genome-wide annotation, expression profiling, and protein interaction studies of the core cell-cycle genes in Phalaenopsis aphrodite. PLANT MOLECULAR BIOLOGY 2014; 84:203-26. [PMID: 24222213 PMCID: PMC3840290 DOI: 10.1007/s11103-013-0128-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/03/2013] [Indexed: 05/06/2023]
Abstract
Orchidaceae is one of the most abundant and diverse families in the plant kingdom and its unique developmental patterns have drawn the attention of many evolutionary biologists. Particular areas of interest have included the co-evolution of pollinators and distinct floral structures, and symbiotic relationships with mycorrhizal flora. However, comprehensive studies to decipher the molecular basis of growth and development in orchids remain scarce. Cell proliferation governed by cell-cycle regulation is fundamental to growth and development of the plant body. We took advantage of recently released transcriptome information to systematically isolate and annotate the core cell-cycle regulators in the moth orchid Phalaenopsis aphrodite. Our data verified that Phalaenopsis cyclin-dependent kinase A (CDKA) is an evolutionarily conserved CDK. Expression profiling studies suggested that core cell-cycle genes functioning during the G1/S, S, and G2/M stages were preferentially enriched in the meristematic tissues that have high proliferation activity. In addition, subcellular localization and pairwise interaction analyses of various combinations of CDKs and cyclins, and of E2 promoter-binding factors and dimerization partners confirmed interactions of the functional units. Furthermore, our data showed that expression of the core cell-cycle genes was coordinately regulated during pollination-induced reproductive development. The data obtained establish a fundamental framework for study of the cell-cycle machinery in Phalaenopsis orchids.
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Affiliation(s)
- Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Miao-Ju Wei
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Yi-Chen Lien
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Huang-Hsien Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Swee-Suak Ko
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Zin-Huang Liu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., Xinshi District, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
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Li X, Luo J, Yan T, Xiang L, Jin F, Qin D, Sun C, Xie M. Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PLoS One 2013; 8:e85480. [PMID: 24392013 PMCID: PMC3877369 DOI: 10.1371/journal.pone.0085480] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022] Open
Abstract
Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.
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Affiliation(s)
- Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Jie Luo
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Tianlian Yan
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Lin Xiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Feng Jin
- College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Dehui Qin
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Ming Xie
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Mondragón-Palomino M. Perspectives on MADS-box expression during orchid flower evolution and development. FRONTIERS IN PLANT SCIENCE 2013; 4:377. [PMID: 24065980 PMCID: PMC3779858 DOI: 10.3389/fpls.2013.00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/03/2013] [Indexed: 05/09/2023]
Abstract
The diverse morphology of orchid flowers and their complex, often deceptive strategies to become pollinated have fascinated researchers for a long time. However, it was not until the 20th century that the ontogeny of orchid flowers, the genetic basis of their morphology and the complex phylogeny of Orchidaceae were investigated. In parallel, the improvement of techniques for in vitro seed germination and tissue culture, together with studies on biochemistry, physiology, and cytology supported the progress of what is now a highly productive industry of orchid breeding and propagation. In the present century both basic research in orchid flower evo-devo and the interest for generating novel horticultural varieties have driven the characterization of many members of the MADS-box family encoding key regulators of flower development. This perspective summarizes the picture emerging from these studies and discusses the advantages and limitations of the comparative strategy employed so far. I address the growing role of natural and horticultural mutants in these studies and the emergence of several model species in orchid evo-devo and genomics. In this context, I make a plea for an increasingly integrative approach.
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Affiliation(s)
- Mariana Mondragón-Palomino
- Department of Cell Biology and Plant Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
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47
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Hsieh MH, Pan ZJ, Lai PH, Lu HC, Yeh HH, Hsu CC, Wu WL, Chung MC, Wang SS, Chen WH, Chen HH. Virus-induced gene silencing unravels multiple transcription factors involved in floral growth and development in Phalaenopsis orchids. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3869-84. [PMID: 23956416 PMCID: PMC3745740 DOI: 10.1093/jxb/ert218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Orchidaceae, one of the largest angiosperm families, has significant commercial value. Isolation of genes involved in orchid floral development and morphogenesis, scent production, and colouration will advance knowledge of orchid flower formation and facilitate breeding new varieties to increase the commercial value. With high-throughput virus-induced gene silencing (VIGS), this study identified five transcription factors involved in various aspects of flower morphogenesis in the orchid Phalaenopsis equestris. These genes are PeMADS1, PeMADS7, PeHB, PebHLH, and PeZIP. Silencing PeMADS1 and PebHLH resulted in reduced flower size together with a pelaloid column containing petal-like epidermal cells and alterations of epidermal cell arrangement in lip lateral lobes, respectively. Silencing PeMADS7, PeHB, and PeZIP alone resulted in abortion of the first three fully developed flower buds of an inflorescence, which indicates the roles of the genes in late flower development. Furthermore, double silencing PeMADS1 and PeMADS6, C- and B-class MADS-box genes, respectively, produced a combinatorial phenotype with two genes cloned in separate vectors. Both PeMADS1 and PeMADS6 are required to ensure the normal development of the lip and column as well as the cuticle formation on the floral epidermal cell surface. Thus, VIGS allows for unravelling the interaction between two classes of MADS transcription factors for dictating orchid floral morphogenesis.
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Affiliation(s)
- Ming-Hsien Hsieh
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Tainan 712Taiwan
| | - Zhao-Jun Pan
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsiang-Chia Lu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung Yeh
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shyh-Shyan Wang
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Tainan 712Taiwan
| | - Wen-Huei Chen
- Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan
- * To whom correspondence should be addressed. E-mail:
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48
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Obayashi T, Yano K. The 2013 Plant and Cell Physiology database issue. PLANT & CELL PHYSIOLOGY 2013; 54:169-170. [PMID: 23396810 DOI: 10.1093/pcp/pct011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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