Core, the core genome; Flexible, the flexible genome; HEG, highly expressed genes; MEG, moderately expressed genes; LEG, lowly expressed

genes; VEG, variably expressed genes. Constantly and this website abundantly expressed transcripts undergo quick degradation Pál et al. previously reported a weak positive association between the rate of evolution and mRNA half-lives in yeast [13]. However, the analysis was done by incomplete genome dataset of RNA degradation. Using a genome-wide mRNA half-life dataset [29], we observed a similar but also slight tendency for genes with lower Ka to selleckchem have shorter half-lives (N = 1262, Spearman’s r = 0.29, P < 0.001). Further investigation showed that highly expressed genes were more likely degraded fast (Figure 7a). Intriguingly, as Steglich et al. reported [29], several genes, including amt1 (ammonium transporter, PMM0263), psbA (PsbA protein D1, PMM0223), som-1/2 (porins, PMM1119 and PMM1121), pcb (light harvesting complex protein, PMM0627), and also two hypothetical genes (HyPMM53 and HyPMM165), that were strongly transcribed turnover very slowly (Figure 7a). This may attribute to these genes’ specific roles in these growth conditions. Despite these exceptions, similar result indicated

that highly expressed transcripts had significant shorter half-lives (Kruskal-Wallis Test, two-tailed PF-562271 chemical structure P < 0.001; Figure 7b). Accordingly, the mRNA turnover rate for genes within the core genome was faster than that of the flexible genome (P < 0.001). Besides for the advantages of rapid recycling nucleotides to adapt to oligotrophic environment [29], fast turnover of HEG might also be beneficial for translation fidelity [52], and consequently make the core genome more economical and compatible with cellular physiology. Figure 7 Correlation between gene expression levels and mRNA half-lives. (a) Correlation between gene expression levels and mRNA half-lives. Red line shows loess-smoothed curve. TCL The exceptions reported by Steglich et

al.[29] were indicated with arrows (b) Box plot of the correlation between gene expression levels and mRNA half-lives (Mann–Whitney U Test, two-tailed). The line was drawn through the median. A circle represents an outlier, and an asterisk represents an extreme data point. Discussion Prochlorococcus is a typical phototroph whose cellular physiology and transcriptome are comprehensively affected by photoperiod [38, 46]. We wondered whether light cycle-influenced gene expression profiles might lead to contradictory conclusions regarding the correlation between gene expression and evolution traits when Prochlorococcus is cultured under constant light conditions. Therefore, we applied the same method we developed to light–dark expression data generated by RNA-Seq [38]. First, we again observed a significant correlation between gene expression levels and corresponding nonsynonymous substitution rates (N = 1275, Spearman’s r = -0.69, P < 0.