Serratia genomics: assembly, annotation and comparative analyses

Abstract

Serratia is a genus of gram-negative bacteria, widespread in nature, important in agricultural, medical and industrial scenarios. Isolates from this taxon exhibits very diverse biological functions such as plant-associated(endophytes, plant growth-promoters, rhizobacteria, phytopathogens), insect-associated(endosymbionts, entomopathogens), fungus-associated (symbionts) and human pathogens.These different lifestylesare determined by the genetic information that each strain carries.The current DNA sequencing technologies provide us data to investigate this variation throughgenomic studies. Therefore, the aim of this work was to study the Serratiagenus using genomic approaches. The biological control agent Serratia marcescens strain N4-5 wassequenced, the nucleotide sequences were assembled into the whole genome andannotated. The N4-5 genome comprises a singular chromosomeof5,074,473bp, with 59.7% GC contentand a naturallyoccurringplasmid. Both sequences were deposited in GenBank database under the accession numbers CP031315 and CP031316. From this newly sequenced genome, in silico comparisons of all other Serratia complete genomes available in GenBankwere performed. Firstly, a taxonomical review of the Serratia genus was conducted based on multi-criteria, namely dDDH, ANI, 16S identity, phylogenetic trees of seven housekeeping genes individually and concatenated (MLSA), as well as phylogenomic tree with whole genomes. Theseanalysisuncovered two misidentifications, supported a recent proposal of a novel Serratia species, confirmed the taxonomic placement of most strains and revealed that many Serratia genomes that are publicly deposited in GenBank are classified incorrectly. These organisms were correctly renamed and the two genomes erroneously identified as Serratia were excluded from the analyses. From these ascertained genomes, an updated pan-, core- and accessory-genomes were constructed. Analysis revealed an open pan-genome and 546 core genes. Descriptions of Serratia spp. genetic organization and presence of secretion systems, secondary metabolites biosynthetic gene clusters, chitinase genes and CRISPR arrays revealed no correlation between genome relatedness and these traits. Analysis of these genomic features evidenced that they are not related with the phenotypes/lifestyles exhibited by Serratia spp. strains. Beyond the new information provided on the plant-beneficial strain S. marcescens N4-5, altogether these results provide better understanding of Serratia at the genus level.