Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55 ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.

Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations

Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing roughly 1–2% of the allergic diseases globally; however, their evolutionary origin, diverse lifestyles including reversible parasitism and quick adaptation to rather new human household environments have not been illustrated at genomic level, which hamper the allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this comparative genomics study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the divergent evolution of astigmatic mites. In the monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases (UGTs), which enriched their capacities of adapting to rapidly changing household environments. The gene diversification after tandem duplications provided plenty of genetic resources for their adaptations of sensing environmental signals, digestion, and detoxification. Whilst many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UGTs and several important fungal cell wall lytic enzymes, which enable the detoxification and associated digestive functions and provide perfect drug targets for pest control. Our comparative study sheds light on the rapid divergent evolution of astigmatic mites from the divergence of Acariformes to their diversification and provides novel insights into the genetic adaptations and even control of human household pests.

Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii and C. flaccumfaciens pv. poinsettiae

Curtobacterium flaccumfaciens complex species in the family Microbacteriaceae encompasses a group of plant pathogenic actinobacterial strains affecting annual crops and ornamental plants. The species includes five pathovars namely C. flaccumfaciens pv. betae, C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. ilicis, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Despite the economic importance of C. flaccumfaciens, its members have rarely been investigated for their phylogenetic relationships, molecular characteristics and virulence repertories due in part to the lack of whole genome resources. Here we present the whole genome sequence of 17 C. flaccumfaciens strains representing members of four pathovars isolated from different plant species in a diverse geographical and temporal span. The genomic data presented in this study will pave the way of research on the comparative genomics, phylogenomics and taxonomy of C. flaccumfaciens, and extend our understanding of the virulence features of the species.

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

Discovery of a class of giant virus relatives displaying unusual functional traits and prevalent within plankton: the Mirusviricetes

Large and giant DNA viruses of the phylum Nucleocytoviricota have a profound influence on the ecology and evolution of planktonic eukaryotes. Recently, various Nucleocytoviricota genomes have been characterized from environmental metagenomes based on the occurrence of hallmark genes identified from cultures. However, lineages diverging from the culture genomics functional principles have been overlooked thus far. Here, we developed a phylogeny-guided genome-resolved metagenomic framework using a single hallmark gene as compass, a subunit of DNA-dependent RNA polymerase encoded by most Nucleocytoviricota. We applied this method to large metagenomic data sets from the surface of five oceans and two seas and characterized 697 non-redundant Nucleocytoviricota genomes up to 1.45 Mbp in length. This database expands the known diversity of the class Megaviricetes and revealed two additional putative classes we named Proculviricetes and Mirusviricetes. Critically, the diverse and prevalent Mirusviricetes population genomes seemingly lack several hallmark genes, in particular those related to viral particle morphogenesis. Instead, they share various genes of known (e.g., TATA-binding proteins, histones, proteases and viral rhodopsins) and unknown functions rarely detected if not entirely missing in all other characterized Nucleocytoviricota lineages. Phylogenomics, comparative genomics, functional trends and the signal among planktonic cellular size fractions point to Mirusviricetes being a major, functionally divergent class of large DNA viruses that actively infect eukaryotes in the sunlit ocean using an enigmatic functional life style. Finally, we built a comprehensive marine genomic database for Nucleocytoviricota by combining multiple environmental surveys that might contribute to future endeavors exploring the ecology and evolution of plankton.

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation, and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation rates for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.