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Open Access Research article

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

Bang Wang1, Lina Lu1, Hexin Lv1, Huifeng Jiang1, Ge Qu1, Chaoguang Tian1* and Yanhe Ma12

Author Affiliations

1 Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China

2 Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

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BMC Microbiology 2014, 14:11  doi:10.1186/1471-2180-14-11

Published: 18 January 2014

Abstract

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.

Keywords:
Core genome; Gene expression; Molecular evolution; Prochlorococcus; RNA-Seq; Transcriptome