Screening of Tissue-Specific Genes and Promoters in Tomato by Comparing Genome Wide Expression Profiles of Arabidopsis Orthologues

Lim, Chan Ju; Lee, Ha Yeon; Kim, Woong Bom; Lee, Bok-Sim; Kim, Jung-Eun; Ahmad, Raza; Kim, Hyun A; Yi, So Young; Hur, Cheol-Goo; Kwon, Suk‐Yoon

doi:10.1007/s10059-012-0068-4

Cited by 22 publications

(14 citation statements)

References 41 publications

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“…4a). This result demonstrated that the methods of Lim et al (2012) are useful for finding tissue-specific genes. We observed the anther at high resolution, and observed that SlPMEI was expressed specifically in the pollen (Fig.…”

Section: Expression Of Slpmei In Reproductive Organs Including Floramentioning

confidence: 75%

“…Isolation and Sequence Analysis of SlPMEI Previously, we applied four screening steps to identify tomato tissue-specific genes. Four screening steps were used for gene isolation: (1) assemble the tomato unigenes from the EST pool using the Sol Genomics Network (SOL Genomic Network; http://sgn.cornell.deu) Stack-pack program using 175 665 tomato ESTs; (2) search Arabidopsis orthologues using blastx in TAIR; (3) screen tissue-specific candidate genes in the Arabidopsis Microarray Database (Genevestigator); (4) validate tissue specificities by RT-PCR and promoter assay (Lim et al 2012). As a result, we identified 311 tissue-specific candidate genes and validated 10 tissue-specific genes in tomato and Arabidopsis.…”

Section: Resultsmentioning

confidence: 99%

“…Previously, Lim et al (2012) observed expression patterns of 311 putative tissue-specific candidate genes in Genevestigator and we chose the candidate of flowerspecific. The Arabidopsis ortholog of the SlPMEI, At1g23350, was expressed in flower, stamen and pollen (Genvestigator; https://www.genevestigator.com/gv/direct link.jsp?geneIDs0At1g23350&tool0T_PRO_AN&source 0genevestigator and Arabidopsis electronic fluorescent pictograph browser; http://bbc.botany.utoronto.ca/efp/ cgi-bin/efpWeb.cgi?primaryGene0At1g23350&mode Input0Absolute).…”

Section: Semi-quantitative Rt-pcr Analysis Of Slpmei In Tomatomentioning

confidence: 99%

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SlPMEI, a pollen-specific gene in tomato

et al. 2014

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2014.SlPMEI, a pollen-specific gene in tomato. Can. J. Plant Sci. 94: 73Á83. Pectin is one of the main components of plant cell walls, and its biosynthesis is controlled by pectin methylesterase (PME). Pectin methylesterase inhibitors (PMEIs) are key regulators of PME. We report here the cloning and characterization of a novel Solanum lycopersicum L. PMEI gene, SlPMEI. RT-PCR studies of leaf, seed, fruit, flower, and flower organs confirmed that SlPMEI is expressed specifically in pollen. Promoter analysis of SlPMEI revealed pollen-specific cis-acting elements (pollen lat52 and g10). In addition, SlPMEI is expressed independently of abiotic stress, pathogen exposure, and growth stage in tomato, and a histochemical analysis of promoter activity revealed pollen-specific expression in both Arabidopsis and tomato. Under the microscope, we observed pollen-specific GUS expression in the stamen of transgenic tomato plant. These results indicate that the promoter of SlPMEI has strong pollen-specific activity, and could therefore be useful for development of industrially and agronomically important transgenic plants. -I. et Kwon, S.-Y. 2014. SlPMEI, un ge`ne spe´cifique au pollen chez la tomate. Can. J. Plant Sci. 94: 73Á83. La pectine est l'un des principaux composants de la paroi cellulaire des plantes et sa biosynthe`se est controˆle´e par la pectine-me´thyleste´rase (PME). Les inhibiteurs de la PME (PMEI) semblent eˆtre les principaux re´gulateurs de la PME. Nous de´crivons le clonage et la caracte´risation d'un nouveau ge`ne PMEI de Solanum lycopersicum L. : SlPMEI. Les e´tudes par RT-PCR de la feuille, de la graine, du fruit et de la fleur, ainsi que des organes de la fleur, ont confirme´que SlPMEI s'exprime spe´cifiquement dans le pollen. L'analyse du promoteur du ge`ne SlPMEI a mis en e´vidence des e´le´ments a`action-cis spe´cifiques du pollen (lat52 et g10 du pollen). De plus, SlPMEI s'exprime inde´pendamment des stress abiotiques, des agents pathoge`nes et des stades de croissance de la tomate, et l'analyse histochimique de l'activite´du promoteur a re´ve´le´une expression spe´cifique au pollen chez Arabidopsis et la tomate. Nous avons observe´au microscope une expression de GUS spe´cifique au pollen dans les e´tamines de plants de tomates transge´niques. Ces re´sultats indiquent que le promoteur de SlPMEI a une forte activiteś pe´cifique au pollen. En outre, ce promoteur spe´cifique au pollen pourrait avoir son utilite´pour le de´veloppement de plants transge´niques importants du point de vue agronomique et industriel.Mots clé s: Tomate, Arabidopsis, SlPMEI promoteur, PMEI, ge`ne spe´cifique au pollen, stressCan.

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Section: Expression Of Slpmei In Reproductive Organs Including Floramentioning

confidence: 75%

Section: Resultsmentioning

confidence: 99%

Section: Semi-quantitative Rt-pcr Analysis Of Slpmei In Tomatomentioning

confidence: 99%

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SlPMEI, a pollen-specific gene in tomato

et al. 2014

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“…Examples of such articles published in the year 2012 include attempts to improve resolution of association mapping using genome-wide studies of quantitative trait loci of an admixture of cultivated cherry tomato and the wild ancestor S. pimpinellifolium (31), and genome-wide ortholog searches for tissue-specific genes and promoters across species (32). Several articles report on genome organization and chromosomal rearrangements in a cross-species comparative context (33).…”

Section: Resultsmentioning

confidence: 99%

From manual curation to visualization of gene families and networks across Solanaceae plant species

et al. 2013

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High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants.Database URL: http://solgenomics.net/

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“…Availability of genome sequences, microarray database, and transcriptome data has enabled rapid identification of orthologous promoters across the plant species (Lim et al, 2012 ; Geng et al, 2014 ). Full-genome array of more and more number of plants has led to the development of several online bioinformatics tools for classification of related sequences and identification of conserved DNA motifs.…”

Section: Introductionmentioning

confidence: 99%

Strength, Stability, and cis-Motifs of In silico Identified Phloem-Specific Promoters in Brassica juncea (L.)

et al. 2016

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Aphids, a hemipteran group of insects pose a serious threat to many of the major crop species including Brassica oilseeds. Transgenic strategies for developing aphid-resistant plant types necessitate phloem-bound expression of the insecticidal genes. A few known phloem-specific promoters, in spite of tissue-specific activity fail to confer high level gene-expression. Here, we identified seven orthologues of phloem-specific promoters in B. juncea (Indian mustard), and experimentally validated their strength of expression in phloem exudates. Significant cis-motifs, globally occurring in phloem-specific promoters showed variable distribution frequencies in these putative phloem-specific promoters of B. juncea. In RT-qPCR based gene-expression study promoter of Glutamine synthetase 3A (GS3A) showed multifold higher activity compared to others, across the different growth stages of B. juncea plants. A statistical method employing four softwares was devised for rapidly analysing stability of the promoter-activities across the plant developmental stages. Different statistical softwares ranked these B. juncea promoters differently in terms of their stability in promoter-activity. Nevertheless, the consensus in output empirically suggested consistency in promoter-activity of the six B. juncea phloem- specific promoters including GS3A. The study identified suitable endogenous promoters for high level and consistent gene-expression in B. juncea phloem exudate. The study also demonstrated a rapid method of assessing species-specific strength and stability in expression of the endogenous promoters.

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Screening of Tissue-Specific Genes and Promoters in Tomato by Comparing Genome Wide Expression Profiles of Arabidopsis Orthologues

Cited by 22 publications

References 41 publications

SlPMEI, a pollen-specific gene in tomato

SlPMEI, a pollen-specific gene in tomato

From manual curation to visualization of gene families and networks across Solanaceae plant species

Strength, Stability, and cis-Motifs of In silico Identified Phloem-Specific Promoters in Brassica juncea (L.)

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