(Penny) Chisholm of MIT for offering CT a short visit to her laboratory and for kind suggestions on Prochlorococcus work. We are also grateful to Allison Coe for help provided during CT’s short visit to Chisholm’s lab. We also thank Yuan Li, Pingping Wang, and Pengpeng Li for technical discussions. This work was supported by the 973 this website Program of China (2011CBA00800 and 2013CB733600), Project INK1197 clinical trial of Chinese Academy of Sciences (KSCX2-EW-G-8) and 863 Program of China (2012AA022203D). Electronic supplementary

material Additional file 1: Operons (harboring at least two genes) of Prochlorococcus MED4. (XLSX 63 KB) Additional file 2: UTRs of Prochlorococcus MED4. Sheet 1: 5’UTRs; sheet 2: 3’UTRs. (XLSX 93 KB) Additional file 3: RNA sequencing profiles and gene expression. Sheet 1: summary of RNA-Seq for ten samples; sheet 2: gene annotations from MicrobesOnline [63] and expression classification; sheet 3: expression values SAHA HDAC cell line of the whole genome. (XLSX 645 KB) Additional file 4: Novel ORFs and ncRNAs. (XLSX 14 KB) Additional file 5: Correlation between the gene expression levels and nonsynonymous substitution

rates (Ka) based on light–dark RNA-Seq data[38]. RPKM, reads per kilobase per million mapped reads; number of pairwise protein = 1275, Spearman’s r = -0.69, P < 0.001. (PDF 560 KB) Additional file 6: Gene expression and molecular evolution of the core genome and flexible genome of Prochlorococcus MED4 based on light–dark RNA-Seq data[38]. (a) Box plot of the correlation between gene expression levels and the nonsynonymous substitution Phloretin rates (Ka). The line was drawn through the median. A circle represents an outlier, and an asterisk represents an extreme data point. (b) Nonsynonymous substitution rate comparison between CEG and VEG (Mann–Whitney U Test, two-tailed). A circle represents an outlier, and an asterisk represents an extreme data point. (c)

Comparisons of five expression subclasses between the core genome and flexible genome (Fisher’s exact test, one-tailed). P-value ≤ 0.05 was indicated in figure. HEG, highly expressed genes; MEG, moderately expressed genes; LEG, lowly expressed genes; NEG, non expressed genes; CEG, constantly expressed genes (including four expression subclasses mentioned above); VEG, variably expressed genes. (PDF 435 KB) Additional file 7: Correlation between gene expression levels and mRNA half-lives based on light–dark RNA-Seq data[38]. (a) Correlation between gene expression levels and mRNA half-lives. Red line shows loess-smoothed curve. The exceptions reported by Steglich et al. 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. (PDF 667 KB) Additional file 8: Gene expression and molecular evolution of the core genome and flexible genome of Prochlorococcus MED4 based on iron-stress microarray data[53].