Enome Biology 2010, 11:R85 http://genomebiology.com/2010/11/8/RPage 13 ofFigure 8 Radar plot showing
Enome Biology 2010, 11:R85 http://genomebiology.com/2010/11/8/RPage 13 ofFigure 8 Radar plot Pinometostat supplier showing the preference of C ending codons, obtained from Codon Adaptation Index analysis done on highly expressed transcripts only. Codons shown in red correspond to the most commonly used codons.demonstrate clearly PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 the biological significance of the measured transciptional outputs – for example, the nitrogen limited libraries show clear effects in genes involved in nitrogen metabolism. Our analyses are especially valuable for the exploration of diatom genes with undefined functions because expression profiling can shed light on their functional significance [49]. Many of these genes encode proteins that lack recognizable InterPro domains, and have been classified as encoding POFs. Diatom genomes encode higher numbers of POFs than have been observed in other genomes (see Results). In rice and Arabidopsis, such genes are thought to contribute to ecologicaldifferences and species diversity [37,38]. The predicted biochemical characteristics of these putative P. tricornutum proteins suggest that they represent functional proteins. Approximately half of them are also found in T. pseudonana, and interestingly can be seen in many cases to be specifically induced by high decadienal treatment (Figure 6; Additional file 11). This aldehyde is of interest because it has been implicated in regulating diatom population densities [20,50], so these genes deserve attention as being of potential importance in the control of population density and programmed cell death. The different statistical methods employed in this study provide support for several recent hypothesesMaheswari et al. Genome Biology 2010, 11:R85 http://genomebiology.com/2010/11/8/RPage 14 ofproposed on the basis of experimental observations; for example, the commonalities of nitrate, ammonium and urea assimilation [7,43] can be seen in the similar expression profiles of the NS, AA, and UA libraries, and the reprogramming of diatom photosynthesis in response to iron limitation [33] is reflected in the common gene expression profiles between the FL library and the blue light (BL) library (Figure 2). Conversely, the two abiotic stress libraries – low temperature (TA) and low salinity (OM) – display similar expression profiles (Figure 2), in agreement with the known overlap in the response to these stresses in other organisms [8]. These expected results are satisfying, but more importantly they increase confidence that the methodologies used can help resolve other less well understood processes involved in each individual response. For example, when hierarchical clustering is done using only the small set of 177 expressed transcription factors in P. tricornutum, the relationships observed between the different libraries are essentially the same as can be seen when using all 9,145 TUs [17] (Figure 2). Hence, the methodologies reported here can help identify transcription factors associated with differential expression in the different growth conditions. Conversely, genes of unknown function can be recruited to a specific response, for example, those induced in response to high decadienal. Such correlations provide a reasonable basis to explore the function of such genes. Finally, our studies have helped to understand better the roles in diatoms of genes of probable bacterial origin. These acquired bacterial genes have undergone modifications, such as gene fusions and novel domain reorganizations [8].