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Lin L, Cai W, Du Z, Zhang W, Xu Q, Sun W, Chen M. Establishing a System for Functional Characterization of Full-Length cDNAs of Camellia sinensis. Int J Mol Sci 2019; 20:ijms20235929. [PMID: 31775391 PMCID: PMC6929147 DOI: 10.3390/ijms20235929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis) is enriched with bioactive secondary metabolites, and is one of the most popular nonalcoholic beverages globally. Two tea reference genomes have been reported; however, the functional analysis of tea genes has lagged, mainly due to tea’s recalcitrance to genetic transformation and the absence of alternative high throughput heterologous expression systems. A full-length cDNA collection with a streamlined cloning system is needed in this economically important woody crop species. RNAs were isolated from nine different vegetative tea tissues, pooled, then used to construct a normalized full-length cDNA library. The titer of unamplified and amplified cDNA library was 6.89 × 106 and 1.8 × 1010 cfu/mL, respectively; the library recombinant rate was 87.2%. Preliminary characterization demonstrated that this collection can complement existing tea reference genomes and facilitate rare gene discovery. In addition, to streamline tea cDNA cloning and functional analysis, a binary vector (pBIG2113SF) was reengineered, seven tea cDNAs isolated from this library were successfully cloned into this vector, then transformed into Arabidopsis. One FL-cDNA, which encodes a putative P1B-type ATPase 5 (CsHMA5), was characterized further as a proof of concept. We demonstrated that overexpression of CsHMA5 in Arabidopsis resulted in copper hyposensitivity. Thus, our data demonstrated that this represents an efficient system for rare gene discovery and functional characterization of tea genes. The integration of a tea FL-cDNA collection with efficient cloning and a heterologous expression system would facilitate functional annotation and characterization of tea genes.
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Affiliation(s)
- Lin Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weiwei Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Zhenghua Du
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Wenjing Zhang
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weijiang Sun
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| | - Mingjie Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
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Liu M, He X, Feng T, Zhuo R, Qiu W, Han X, Qiao G, Zhang D. cDNA Library for Mining Functional Genes in Sedum alfredii Hance Related to Cadmium Tolerance and Characterization of the Roles of a Novel SaCTP2 Gene in Enhancing Cadmium Hyperaccumulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10926-10940. [PMID: 31449747 DOI: 10.1021/acs.est.9b03237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Heavy metal contamination presents serious threats to living organisms. Functional genes related to cadmium (Cd) hypertolerance or hyperaccumulation must be explored to enhance phytoremediation. Sedum alfredii Hance is a Zn/Cd cohyperaccumulator exhibiting abundant genes associated with Cd hypertolerance. Here, we developed a method for screening genes related to Cd tolerance by expressing a cDNA-library for S. alfredii Hance. Yeast functional complementation validated 42 of 48 full-length genes involved in Cd tolerance, and the majority of them were strongly induced in roots and exhibited diverse expression profiles across tissues. Coexpression network analysis suggested that 15 hub genes were connected with genes involved in metabolic processes, response to stimuli, and metal transporter and antioxidant activity. The functions of a novel SaCTP2 gene were validated by heterologous expression in Arabidopsis, responsible for retarding chlorophyll content decrease, maintaining membrane integrity, promoting reactive oxygen species (ROS) scavenger activities, and reducing ROS levels. Our findings suggest a highly complex network of genes related to Cd hypertolerance in S. alfredii Hance, accomplished via the antioxidant system, defense genes induction, and the calcium signaling pathway. The proposed cDNA-library method is an effective approach for mining candidate genes associated with Cd hypertolerance to develop genetically engineered plants for use in phytoremediation.
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Affiliation(s)
- Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
- School of Basic Medical Sciences , Zhejiang Chinese Medical University , Hangzhou 310053 , People's Republic of China
| | - Xuelian He
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Tongyu Feng
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , People's Republic of China
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López-Pérez M, Ballester AR, González-Candelas L. Identification and functional analysis of Penicillium digitatum genes putatively involved in virulence towards citrus fruit. MOLECULAR PLANT PATHOLOGY 2015; 16:262-75. [PMID: 25099378 PMCID: PMC6638479 DOI: 10.1111/mpp.12179] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The fungus Penicillium digitatum, the causal agent of green mould rot, is the most destructive post-harvest pathogen of citrus fruit in Mediterranean regions. In order to identify P. digitatum genes up-regulated during the infection of oranges that may constitute putative virulence factors, we followed a polymerase chain reaction (PCR)-based suppression subtractive hybridization and cDNA macroarray hybridization approach. The origin of expressed sequence tags (ESTs) was determined by comparison against the available genome sequences of both organisms. Genes coding for fungal proteases and plant cell wall-degrading enzymes represent the largest categories in the subtracted cDNA library. Northern blot analysis of a selection of P. digitatum genes, including those coding for proteases, cell wall-related enzymes, redox homoeostasis and detoxification processes, confirmed their up-regulation at varying time points during the infection process. Agrobacterium tumefaciens-mediated transformation was used to generate knockout mutants for two genes encoding a pectin lyase (Pnl1) and a naphthalene dioxygenase (Ndo1). Two independent P. digitatum Δndo1 mutants were as virulent as the wild-type. However, the two Δpnl1 mutants analysed were less virulent than the parental strain or an ectopic transformant. Together, these results provide a significant advance in our understanding of the putative determinants of the virulence mechanisms of P. digitatum.
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Affiliation(s)
- Mario López-Pérez
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Calle Catedrático Agustín Escardino 7, Paterna, 46980, Valencia, Spain
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Pinheiro TT, Figueira A, Latado RR. Early-flowering sweet orange mutant 'x11' as a model for functional genomic studies of Citrus. BMC Res Notes 2014; 7:511. [PMID: 25108567 PMCID: PMC4267115 DOI: 10.1186/1756-0500-7-511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There had been many reports on genetic transformation of Citrus for functional genomic studies but few included genes associated with flower or fruit traits. A major reason for this might derive from the extensive juvenile stage of Citrus plants when regenerated from juvenile explants (epicotyls, cotyledon or calli), which delays the observation of the resulting phenotype. Alternatives include the use of explants from adult tissues, which sometimes may be recalcitrant to regeneration or transformation, or of early-flowering genotypes. However, there is no report about the use of early-flowering sweet orange mutants for functional genomic studies. RESULTS Here, we propose a sweet orange spontaneous early-flowering mutant, named 'x11', as a platform for Citrus functional genomic studies, particularly for genes associated with flower or fruit traits. We report a procedure for efficient regeneration and transformation using epicotyl segment explants of 'x11' and Agrobacterium tumefaciens as a proof-of-concept. The average transformation efficiency was 18.6%, but reached 29.6% in the best protocol tested. Among 270 positive shoots, five were in vitro micrografted and acclimatized, followed by evaluation of transgene expression by quantitative amplification of reversed transcripts (RT-qPCR) and determination of the number of copies inserted. Four of these plants, containing from one to four copies of the transgene, exhibited the first flowers within three months after ex vitro establishment, and the other, two months later, regardless of the period of the year. Flowers of transgenic plants displayed fertile pollen and gynoecium, with self-pollination inducing fruit development with seeds. Histochemical staining for β-glucuronidase activity using stem segments, flowers and fruits from 5 to 7 month-old acclimatized transgenic plants confirmed the constitutive transgene expression in these organs. CONCLUSION The 'x11' sweet orange is suitable for functional genomics studies with a satisfactory transformation rate, and it can be considered a good model for functional genomic studies in commercial sweet oranges, for traits related to flower and fruit.
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Affiliation(s)
- Thaísa Tessutti Pinheiro
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
| | - Antonio Figueira
- />Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP 13400-970 Brazil
| | - Rodrigo Rocha Latado
- />Centro de Citricultura “Sylvio Moreira”, Instituto Agronômico, CP 04, Cordeirópolis, SP 13490-970 Brazil
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Ramegowda V, Senthil-kumar M, Udayakumar M, Mysore KS. A high-throughput virus-induced gene silencing protocol identifies genes involved in multi-stress tolerance. BMC PLANT BIOLOGY 2013; 13:193. [PMID: 24289810 PMCID: PMC3879149 DOI: 10.1186/1471-2229-13-193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/21/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND Understanding the function of a particular gene under various stresses is important for engineering plants for broad-spectrum stress tolerance. Although virus-induced gene silencing (VIGS) has been used to characterize genes involved in abiotic stress tolerance, currently available gene silencing and stress imposition methodology at the whole plant level is not suitable for high-throughput functional analyses of genes. This demands a robust and reliable methodology for characterizing genes involved in abiotic and multi-stress tolerance. RESULTS Our methodology employs VIGS-based gene silencing in leaf disks combined with simple stress imposition and effect quantification methodologies for easy and faster characterization of genes involved in abiotic and multi-stress tolerance. By subjecting leaf disks from gene-silenced plants to various abiotic stresses and inoculating silenced plants with various pathogens, we show the involvement of several genes for multi-stress tolerance. In addition, we demonstrate that VIGS can be used to characterize genes involved in thermotolerance. Our results also showed the functional relevance of NtEDS1 in abiotic stress, NbRBX1 and NbCTR1 in oxidative stress; NtRAR1 and NtNPR1 in salinity stress; NbSOS1 and NbHSP101 in biotic stress; and NtEDS1, NbETR1, NbWRKY2 and NbMYC2 in thermotolerance. CONCLUSIONS In addition to widening the application of VIGS, we developed a robust, easy and high-throughput methodology for functional characterization of genes involved in multi-stress tolerance.
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Affiliation(s)
- Venkategowda Ramegowda
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK 73402, USA
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560 065Karnataka, India
- Present address: VR: Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701 USA; MS: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Muthappa Senthil-kumar
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK 73402, USA
- Present address: VR: Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701 USA; MS: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Makarla Udayakumar
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560 065Karnataka, India
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK 73402, USA
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Transcriptome generation and analysis from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758) through normalized cDNA library. Mol Biol Rep 2013; 40:6965-75. [DOI: 10.1007/s11033-013-2816-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 10/16/2013] [Indexed: 01/13/2023]
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Biotechnological approaches to study plant responses to stress. BIOMED RESEARCH INTERNATIONAL 2012; 2013:654120. [PMID: 23509757 PMCID: PMC3591138 DOI: 10.1155/2013/654120] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/30/2012] [Indexed: 12/01/2022]
Abstract
Multiple biotic and abiotic environmental stress factors affect negatively various aspects of plant growth, development, and crop productivity. Plants, as sessile organisms, have developed, in the course of their evolution, efficient strategies of response to avoid, tolerate, or adapt to different types of stress situations. The diverse stress factors that plants have to face often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, upregulation of the antioxidant machinery, and accumulation of compatible solutes. Over the last few decades advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to abiotic stress conditions. In this paper, recent progresses on systematic analyses of plant responses to stress including genomics, proteomics, metabolomics, and transgenic-based approaches are summarized.
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Ma J, Wei H, Song M, Pang C, Liu J, Wang L, Zhang J, Fan S, Yu S. Transcriptome profiling analysis reveals that flavonoid and ascorbate-glutathione cycle are important during anther development in Upland cotton. PLoS One 2012; 7:e49244. [PMID: 23155472 PMCID: PMC3498337 DOI: 10.1371/journal.pone.0049244] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 10/04/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Previous transcriptome profiling studies have investigated the molecular mechanisms of pollen and anther development, and identified many genes involved in these processes. However, only 51 anther ESTs of Upland cotton (Gossypium hirsutum) were found in NCBI and there have been no reports of transcriptome profiling analyzing anther development in Upland cotton, a major fiber crop in the word. METHODOLOGY/PRINCIPAL FINDING Ninety-eight hundred and ninety-six high quality ESTs were sequenced from their 3'-ends and assembled into 6,643 unigenes from a normalized, full-length anther cDNA library of Upland cotton. Combined with previous sequenced anther-related ESTs, 12,244 unigenes were generated as the reference genes for digital gene expression (DGE) analysis. The DGE was conducted on anthers that were isolated at tetrad pollen (TTP), uninucleate pollen (UNP), binucleate pollen (BNP) and mature pollen (MTP) periods along with four other tissues, i.e., roots (RO), stems (ST), leaves (LV) and embryos (EB). Through transcriptome profiling analysis, we identified 1,165 genes that were enriched at certain anther development periods, and many of them were involved in starch and sucrose metabolism, pentose and glucuronate interconversion, flavonoid biosynthesis, and ascorbate and aldarate metabolism. CONCLUSIONS/SIGNIFICANCE We first generated a normalized, full-length cDNA library from anthers and performed transcriptome profiling analysis of anther development in Upland cotton. From these results, 10,178 anther expressed genes were identified, among which 1,165 genes were stage-enriched in anthers. And many of these stage-enriched genes were involved in some important processes regulating anther development.
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Affiliation(s)
- Jianhui Ma
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Ji Liu
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Long Wang
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
- * E-mail: (SF); (SY)
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
- * E-mail: (SF); (SY)
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Roslan ND, Yusop JM, Baharum SN, Othman R, Mohamed-Hussein ZA, Ismail I, Noor NM, Zainal Z. Flavonoid biosynthesis genes putatively identified in the aromatic plant Polygonum minus via Expressed Sequences Tag (EST) analysis. Int J Mol Sci 2012; 13:2692-2706. [PMID: 22489118 PMCID: PMC3317681 DOI: 10.3390/ijms13032692] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 11/16/2022] Open
Abstract
P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic data, the biosynthetic pathway of flavonoids is currently unclear. Identification of candidate genes involved in the flavonoid biosynthetic pathway will significantly contribute to understanding the biosynthesis of active compounds. We have constructed a standard cDNA library from P. minus leaves, and two normalized full-length enriched cDNA libraries were constructed from stem and root organs in order to create a gene resource for the biosynthesis of secondary metabolites, especially flavonoid biosynthesis. Thus, large-scale sequencing of P. minus cDNA libraries identified 4196 expressed sequences tags (ESTs) which were deposited in dbEST in the National Center of Biotechnology Information (NCBI). From the three constructed cDNA libraries, 11 ESTs encoding seven genes were mapped to the flavonoid biosynthetic pathway. Finally, three flavonoid biosynthetic pathway-related ESTs chalcone synthase, CHS (JG745304), flavonol synthase, FLS (JG705819) and leucoanthocyanidin dioxygenase, LDOX (JG745247) were selected for further examination by quantitative RT-PCR (qRT-PCR) in different P. minus organs. Expression was detected in leaf, stem and root. Gene expression studies have been initiated in order to better understand the underlying physiological processes.
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Affiliation(s)
- Nur Diyana Roslan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia,43600 Bangi Selangor, Malaysia
| | - Jastina Mat Yusop
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
| | - Roohaida Othman
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia,43600 Bangi Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia,43600 Bangi Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
| | - Zamri Zainal
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia; E-Mails: (N.D.R.); (J.M.Y.); (S.N.B.); (R.O.); (Z.-A.M.-H.); (I.I.); (N.M.N.)
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia,43600 Bangi Selangor, Malaysia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +60-89213387; Fax: +60-89214769
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Marques MC, Perez-Amador MA. Construction and analysis of full-length and normalized cDNA libraries from citrus. Methods Mol Biol 2012; 815:51-65. [PMID: 22130983 DOI: 10.1007/978-1-61779-424-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed an integrated method to generate a normalized cDNA collection enriched in full-length and rare transcripts from citrus, using different species and multiple tissues and developmental stages. Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. In this regard, the availability of full-length cDNA clones facilitates functional analysis of the corresponding genes enabling manipulation of their expression and the generation of a variety of tagged versions of the native protein. The development of full-length cDNA sequences has the power to improve the quality of genome annotation, as well as provide tools for functional characterization of genes.
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Affiliation(s)
- M Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas-IBMCP, Universidad Politécnica de Valencia-UPV and Consejo Superior de Investigaciones Científicas-CSIC, CPI 8E, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
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Xia JH, He XP, Bai ZY, Lin G, Yue GH. Analysis of the Asian seabass transcriptome based on expressed sequence tags. DNA Res 2011; 18:513-22. [PMID: 22086997 PMCID: PMC3223082 DOI: 10.1093/dnares/dsr036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Analysis of transcriptomes is of great importance in genomic studies. Asian seabass is an important fish species. A number of genomic tools in it were developed, while large expressed sequence tag (EST) data are lacking. We sequenced ESTs from nine normalized cDNA libraries and obtained 11 431 high-quality ESTs. We retrieved 8524 ESTs from dbEST database and analyzed all 19 975 ESTs using bioinformatics tools. After clustering, we obtained 8837 unique sequences (2838 contigs and 5999 singletons). The average contig length was 574 bp. Annotation of these unique sequences revealed that 48.9% of them showed significant homology to RNA sequences in GenBank. Functional classification of the unique ESTs identified a broad range of genes involved in different functions. We identified 6114 putative single-nucleotide polymorphisms and 634 microsatellites in ESTs. We discovered different temporal and spatial expression patterns of some immune-related genes in the Asian seabass after challenging with a pathogen Vibrio harveyi. The unique EST sequences are being used in developing a cDNA microarray to examine global gene expression and will also facilitate future whole-genome sequence assembly and annotation of Asian seabass and comparative genomics.
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Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore
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Enrique R, Siciliano F, Favaro MA, Gerhardt N, Roeschlin R, Rigano L, Sendin L, Castagnaro A, Vojnov A, Marano MR. Novel demonstration of RNAi in citrus reveals importance of citrus callose synthase in defence against Xanthomonas citri subsp. citri. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:394-407. [PMID: 20809929 DOI: 10.1111/j.1467-7652.2010.00555.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Citrus is an economically important fruit crop that is severely afflicted by citrus canker, a disease caused by the bacterial phytopathogen, Xanthomonas citri subsp. citri (Xcc). GenBank houses a large collection of Expressed Sequence Tags (ESTs) enriched with transcripts generated during the defence response against this pathogen; however, there are currently no strategies in citrus to assess the function of candidate genes. This has greatly limited research as defence signalling genes are often involved in multiple pathways. In this study, we demonstrate the efficacy of RNA interference (RNAi) as a functional genomics tool to assess the function of candidate genes involved in the defence response of Citrus limon against the citrus canker pathogen. Double-stranded RNA expression vectors, encoding hairpin RNAs for citrus host genes, were delivered to lemon leaves by transient infiltration with transformed Agrobacterium. As proof of principle, we have established silencing of citrus phytoene desaturase (PDS) and callose synthase (CalS1) genes. Phenotypic and molecular analyses showed that silencing vectors were functional not only in lemon plants but also in other species of the Rutaceae family. Using silencing of CalS1, we have demonstrated that plant cell wall-associated defence is the principal initial barrier against Xanthomonas infection in citrus plants. Additionally, we present here results that suggest that H₂O₂ accumulation, which is suppressed by xanthan from Xcc during pathogenesis, contributes to inhibition of xanthan-deficient Xcc mutant growth either in wild-type or CalS1-silenced plants. With this work, we have demonstrated that high-throughput reverse genetic analysis is feasible in citrus.
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Affiliation(s)
- Ramón Enrique
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha, Rosario, Argentina
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Mondego JMC, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GGL, Pereira LFP, Andrade AC, Colombo CA, Vieira LGE, Pereira GAG. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC PLANT BIOLOGY 2011; 11:30. [PMID: 21303543 PMCID: PMC3045888 DOI: 10.1186/1471-2229-11-30] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 02/08/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. RESULTS Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. CONCLUSION We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
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Affiliation(s)
- Jorge MC Mondego
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Laboratório Nacional de Biociências (LNBio), CP 6192, 13083-970, Campinas-SP, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, CP 6141, 13083-970, Campinas, SP, Brazil
| | - Eric K Tokuda
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Lucas P Parizzi
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Gustavo GL Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Luiz FP Pereira
- Embrapa Café - Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, 86001-970, Londrina-PR, Brazil
| | - Alan C Andrade
- Núcleo de Biotecnologia-NTBio, Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, 70770-900, Brasília-DF, Brazil
| | - Carlos A Colombo
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Luiz GE Vieira
- Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, CEP 86001-970, Londrina-PR, Brazil
| | - Gonçalo AG Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
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Zhang JZ, Ai XY, Sun LM, Zhang DL, Guo WW, Deng XX, Hu CG. Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. BMC Genomics 2011; 12:63. [PMID: 21269450 PMCID: PMC3039610 DOI: 10.1186/1471-2164-12-63] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 01/26/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about the molecular processes regulating flowering transition in woody plants compared with herbaceous plants. RESULTS Comparative transcript profiling of spring shoots after self-pruning was performed on a spontaneously early flowering trifoliate orange mutant (precocious trifoliate orange, Poncirus trifoliata) with a short juvenile phase and the wild-type (WT) tree by using massively parallel signature sequencing (MPSS). A total of 16,564,500 and 16,235,952 high quality reads were obtained for the WT and the mutant (MT), respectively. Interpretation of the MPSS signatures revealed that the total number of transcribed genes in the MT (31,468) was larger than in the WT (29,864), suggesting that newly initiated transcription occurs in the MT. Further comparison of the transcripts revealed that 2735 genes had more than twofold expression difference in the MT compared with the WT. In addition, we identified 110 citrus flowering-time genes homologous with known elements of flowering-time pathways through sequencing and bioinformatics analysis. These genes are highly conserved in citrus and other species, suggesting that the functions of the related proteins in controlling reproductive development may be conserved as well. CONCLUSION Our results provide a foundation for comparative gene expression studies between WT and precocious trifoliate orange. Additionally, a number of candidate genes required for the early flowering process of precocious trifoliate orange were identified. These results provide new insight into the molecular processes regulating flowering time in citrus.
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Affiliation(s)
- Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiao-Yan Ai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lei-Ming Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
| | | | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China
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Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA, Singh KK, Madasamy P. Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds. BMC Genomics 2010; 11:606. [PMID: 20979643 PMCID: PMC3091748 DOI: 10.1186/1471-2164-11-606] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 10/27/2010] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs). RESULTS A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes. CONCLUSIONS The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.
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Affiliation(s)
- Purushothaman Natarajan
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, 603 203, India
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Mochida K, Shinozaki K. Genomics and bioinformatics resources for crop improvement. PLANT & CELL PHYSIOLOGY 2010; 51:497-523. [PMID: 20208064 PMCID: PMC2852516 DOI: 10.1093/pcp/pcq027] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 03/01/2010] [Indexed: 05/19/2023]
Abstract
Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.
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