Pan-genome analysis of six completeParacoccustype strain genomes from hybrid next generation sequencing

Abstract

AbstractThe genusParacoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial is globally distributed. In addition,Paracoccusis taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on howParacoccuscan adapt to such a range of different ecological niches and lifestyles. In the present study, the genusParacoccuswas phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassifiedParacoccussp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis ofParacoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish,Bugula plumosa, and the reef-building coralStylophora pistillatato elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes werede novohybrid assembled using a combination of short and long-read technologies. TheseParacoccusgenomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84 %) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free- living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Due to the vast number of adaptive genes,Paracoccuscan quickly adapt to changing environmental conditions.