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Background  Gene gain and loss frequently occurs in the cyanobacterium  Prochlorococcus , a phototroph that numerically dominates tropical and subtropical open oceans. However, little is known about the stabilization of its core genome, which contains approximately 1250 genes, in the context of genome streamlining. Using  Prochlorococcus  MED4 as a model organism, we investigated the constraints on core genome stabilization using transcriptome profiling.    Results  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.    Conclusions  Gene expression, gene necessity, and mRNA turnover contribute to core genome maintenance during cyanobacterium  Prochlorococcus  genus evolution.

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