Abstract
BackgroundGene 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.ResultsRNA-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.ConclusionsGene expression, gene necessity, and mRNA turnover contribute to core genome maintenance during cyanobacterium Prochlorococcus genus evolution.
Highlights
Gene gain and loss frequently occurs in the cyanobacterium Prochlorococcus, a phototroph that numerically dominates tropical and subtropical open oceans
Transcriptome structure of Prochlorococcus MED4 The Illumina high-throughput sequencing (RNA-Seq) protocols were applied to ten Prochlorococcus MED4 samples cultured in Pro99 and artificial medium for Prochlorococcus (AMP) (Table 1; Methods)
Gene expression cut-off was defined as the mean Reads per kilobase per million mapped reads (RPKM) of the ten percentages of the lowest expressed gene regions (Table 1)
Summary
Gene gain and loss frequently occurs in the cyanobacterium Prochlorococcus, a phototroph that numerically dominates tropical and subtropical open oceans. The marine free-living cyanobacterium Prochlorococcus is the most abundant autotroph on our planet, yet its cell size and genome are nearly the smallest among the oxygenic phototrophs [1,2]. This bacterium geographically distributes throughout tropical and subtropical open seas, thriving in oligotrophic regions [2,3]. Kettler et al defined approximately 1250 genes as subspecies Prochlorococcus MED4 has an increased rate of protein evolution and a remarkably reduced genome [7,9,18] These characteristics make it an ideal model organism for examining the evolutionary factors that influence genome evolution
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