In silico prediction of gene expression patterns in Citrus flavedo

Abstract

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.

The Citrus clementina Putative Allergens: From Proteomic Analysis to Structural Features

“…The detection of peptides belonging to Cit cl 1 (clementine0.9_021092m) in all procedures used, and the very high percentage of spectra found for this protein (Tables and , see also Mass Spectrometry and Bioinformatics), validate the hypothesis that Cit cl 1 has high expression level in the peel tissue of clementine fruits, in compliance with high amount of GLPs found in the proteomic analysis of C. limon and in gene expression study of C. sinensis …”

“…The detection of peptides belonging to Cit cl 1 (clementine0.9_021092m) in all procedures used, and the very high percentage of spectra found for this protein (Tables 2 and 3, see also Mass Spectrometry and Bioinformatics), validate the hypothesis that Cit cl 1 has high expression level in the peel tissue of clementine fruits, in compliance with high amount of GLPs found in the proteomic analysis of C. limon 13 and in gene expression study of C. sinensis. 35 Two peptides, with quite a low percentage of spectra, belonging to the putative Cit cl 2 clementine0.9_025303m were obtained following only the procedure 3 (Tables 2 and 3). This finding strongly suggests that the Cit cl 2 profilin has low expression in peel tissue, according to a previous study on sweet orange allergens that showed the accumulation of profilin Cit s 2 mainly in the fruit pulp.…”