Abstract
Viruses and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of CRISPR on genome expansion. In this study, we constructed a comprehensive dataset of prokaryotic genomes and identified their associations with viruses and plasmids. We found that genomes associated with viruses and/or plasmids were significantly larger than those without, indicating that both viruses and plasmids contribute to genome expansion. Genomes were increasingly larger with increasing numbers of associated viruses or plasmids. Conversely, genomes with CRISPR systems were significantly smaller than those without, indicating that CRISPR has a negative impact on genome size. These results confirmed that on evolutionary timescales, viruses and plasmids facilitate genome expansion, while CRISPR impairs such a process in prokaryotes. Furthermore, our results also revealed that CRISPR systems show a preference for targeting viruses over plasmids.
Highlights
Gene duplication and/or horizontal gene transfer (HGT) play important roles in functional innovation and species adaptation, and are the main sources of genome expansions (Isambert and Stein, 2009; Schonknecht et al, 2013; Nyvltova et al, 2015; Smith et al, 2016; Tsai et al, 2018)
Previous studies suggested that the genomic GCcontents as well as nucleotide frequencies of phages and plasmids often closely resembles that of their hosts (Nakashima et al, 2015; Ahlgren et al, 2017; Ren et al, 2017); consistent with these previous observations, we obtained correlation coefficient values of 0.969 and 0.968 between the GC-contents of the host genomes and their associated viruses and plasmids, respectively (Supplementary Figures 1A,B), confirming the high quality of our association data
We found that CRISPRs were enriched in virusassociated compared to plasmid-associated genomes, the significance was only marginal (OR = 1.15, P = 0.08, excluding genomes containing both viruses and plasmids), suggesting a strong target preferences of CRISPRs toward viruses (Table 1)
Summary
Gene duplication and/or horizontal gene transfer (HGT) play important roles in functional innovation and species adaptation, and are the main sources of genome expansions (Isambert and Stein, 2009; Schonknecht et al, 2013; Nyvltova et al, 2015; Smith et al, 2016; Tsai et al, 2018). Mobile DNA elements such as viruses and plasmids can introduce novel DNAs into the host genomes (Yamaguchi et al, 2001; Jensen and Lyon, 2009; Lindsay, 2010; Malachowa and Deleo, 2010). They often have a very narrow range of hosts; but under certain conditions, such as antibiotic stress, viruses and plasmids can expand their host ranges (Modi et al, 2013). Viruses and plasmids are important sources of HGT and of prokaryotic innovations, and drive bacterial evolution and adaptation (Koonin and Wolf, 2008; Nogueira et al, 2009; Argov et al, 2017).
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