In silico prediction of gene expression patterns in Citrus flavedo
Out of the 18,942 flavedo expressed sequences (clusters plus singletons) in Citrus sinensis from the Citrus EST Project (CitEST), 25 were statistically supported to be differentially expressed in this tissue after a double in silico hybridization strategy against leaf-, flower-, and bark-derived ESTs. Five of them, two terpene synthases and three O-methyltransferases, are absent in the other citrus tissues with concomitant 2x2 statistics, supporting the hypothesis that they are putative flavedo-specific expressed sequences. The pattern of these differentially expressed sequences during fruit development suggests that most of them are developmentally regulated. Some expressed gene products, including a putative germin-like protein highly expressed in flavedo, are shown to be promising candidates for further characterization. In addition to promoter seeking, this kind of analysis can lead to gene discovery, tissue-specific and tissue-enriched expression pattern predictions (as shown herein) and can also be adopted as an in silico first, and probably reliable approach, for detecting expression profiles from EST sequencing efforts before experimental validation is available or for heuristically guiding that validation.
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Sociedade Brasileira de Genética
2007
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oai:scielo:S1415-475720070005000042007-11-06In silico prediction of gene expression patterns in Citrus flavedoBerger,Irving J.Freitas-Astúa,JulianaReis,Marcelo S.Targon,Maria Luísa P.N.Machado,Marcos A. EST fruit gene expression orange tissue-specific Out of the 18,942 flavedo expressed sequences (clusters plus singletons) in Citrus sinensis from the Citrus EST Project (CitEST), 25 were statistically supported to be differentially expressed in this tissue after a double in silico hybridization strategy against leaf-, flower-, and bark-derived ESTs. Five of them, two terpene synthases and three O-methyltransferases, are absent in the other citrus tissues with concomitant 2x2 statistics, supporting the hypothesis that they are putative flavedo-specific expressed sequences. The pattern of these differentially expressed sequences during fruit development suggests that most of them are developmentally regulated. Some expressed gene products, including a putative germin-like protein highly expressed in flavedo, are shown to be promising candidates for further characterization. In addition to promoter seeking, this kind of analysis can lead to gene discovery, tissue-specific and tissue-enriched expression pattern predictions (as shown herein) and can also be adopted as an in silico first, and probably reliable approach, for detecting expression profiles from EST sequencing efforts before experimental validation is available or for heuristically guiding that validation.info:eu-repo/semantics/openAccessSociedade Brasileira de GenéticaGenetics and Molecular Biology v.30 n.3 suppl.0 20072007-01-01info:eu-repo/semantics/articletext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500004en10.1590/S1415-47572007000500004 |
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Berger,Irving J. Freitas-Astúa,Juliana Reis,Marcelo S. Targon,Maria Luísa P.N. Machado,Marcos A. |
| spellingShingle |
Berger,Irving J. Freitas-Astúa,Juliana Reis,Marcelo S. Targon,Maria Luísa P.N. Machado,Marcos A. In silico prediction of gene expression patterns in Citrus flavedo |
| author_facet |
Berger,Irving J. Freitas-Astúa,Juliana Reis,Marcelo S. Targon,Maria Luísa P.N. Machado,Marcos A. |
| author_sort |
Berger,Irving J. |
| title |
In silico prediction of gene expression patterns in Citrus flavedo |
| title_short |
In silico prediction of gene expression patterns in Citrus flavedo |
| title_full |
In silico prediction of gene expression patterns in Citrus flavedo |
| title_fullStr |
In silico prediction of gene expression patterns in Citrus flavedo |
| title_full_unstemmed |
In silico prediction of gene expression patterns in Citrus flavedo |
| title_sort |
in silico prediction of gene expression patterns in citrus flavedo |
| description |
Out of the 18,942 flavedo expressed sequences (clusters plus singletons) in Citrus sinensis from the Citrus EST Project (CitEST), 25 were statistically supported to be differentially expressed in this tissue after a double in silico hybridization strategy against leaf-, flower-, and bark-derived ESTs. Five of them, two terpene synthases and three O-methyltransferases, are absent in the other citrus tissues with concomitant 2x2 statistics, supporting the hypothesis that they are putative flavedo-specific expressed sequences. The pattern of these differentially expressed sequences during fruit development suggests that most of them are developmentally regulated. Some expressed gene products, including a putative germin-like protein highly expressed in flavedo, are shown to be promising candidates for further characterization. In addition to promoter seeking, this kind of analysis can lead to gene discovery, tissue-specific and tissue-enriched expression pattern predictions (as shown herein) and can also be adopted as an in silico first, and probably reliable approach, for detecting expression profiles from EST sequencing efforts before experimental validation is available or for heuristically guiding that validation. |
| publisher |
Sociedade Brasileira de Genética |
| publishDate |
2007 |
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http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500004 |
| work_keys_str_mv |
AT bergerirvingj insilicopredictionofgeneexpressionpatternsincitrusflavedo AT freitasastuajuliana insilicopredictionofgeneexpressionpatternsincitrusflavedo AT reismarcelos insilicopredictionofgeneexpressionpatternsincitrusflavedo AT targonmarialuisapn insilicopredictionofgeneexpressionpatternsincitrusflavedo AT machadomarcosa insilicopredictionofgeneexpressionpatternsincitrusflavedo |
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1756419013580161024 |