The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome

RNA-Seq technique was used to obtain the transcriptome map of Prochlorococcus MED4, including operons, untranslated regions, non-coding RNAs, and novel genes. Genome-wide expression profiles revealed that three factors contribute to core genome stabilization. First, a negative correlation between gene expression levels and protein evolutionary rates was observed. Highly expressed genes were overrepresented in the core genome but not in the flexible genome. Gene necessity was determined as a second powerful constraint on genome evolution through functional enrichment analysis. Third, quick mRNA turnover may increase corresponding proteins’ fidelity among genes that were abundantly expressed. Together, these factors influence core genome stabilization during MED4 genome evolution. Overall design: The cells were cultured on Pro99 medium for a certain time course (1, 3, 4, 8, and 10 days); or transferred to AMP (Artificial Medium for Prochlorococcus) with 6 mM or 24 mM sodium bicarbonate for 5 or 10 hours.