Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

Abstract

Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection.

Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure

“…Specifically, the JC model was selected for the dnak gene, the JC+modelГ for efp , the T92 model for fumC , the K2 model for glyA , rpoD and trpB , and the HKY model for murG . Analysis using the BMCMC method returned a partial phylogeny for the P. salmonis strains; this phylogeny was consistent with previous reconstructions of P. salmonis strains isolated from Chilean salmonids (Nourdin‐Galindo et al, ; Otterlei et al, ; Saavedra et al, ). Phylogenetic reconstructions with individual and concatenated genes were congruent in separating the LF‐89 T and EM‐90 genogroups.…”

“…Seven housekeeping gene loci were selected for MLST, including dnaK , efp , fumC , glyA , murG , rpoD and trpB . These genes chosen based on the genome sequences of P. salmonis LF‐89 T (Eppinger et al, ) and AUSTRAL‐005 (Yañez et al, ) and other P. salmonis isolates publicly available and published by our group in the pan‐genome analysis of this bacterium (Nourdin‐Galindo et al, ). The primer pairs were designed using the online Primer 3 software (http://www.ncbi.nlm.nih.gov/tools/primer-blast/).…”

Addressing viral and bacterial threats to salmon farming in Chile: historical contexts and perspectives for management and control

“…The obtained data suggest that these genes could be directly associated with inter‐genogroup differences in pathogenesis and host‐pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection (Nourdin‐Galindo et al . ).…”

“…To address this knowledge gap, Nourdin‐Galindo et al . () conducted an in silico pan‐genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan‐genome of ~3400 genes and a core‐genome of ~1700 genes.…”

Factors associated with severity of naturally occurring piscirickettsiosis in netpen‐ and tank‐reared juvenile Atlantic salmon at a research aquarium in western Canada

“…For each qPCR run, the number of copies per reaction (c/rxn) was determined from a standard curve generated by amplifying a 10‐fold serially diluted double‐stranded DNA gBLOCK fragment (IDT Technologies) which included the P. salmonis primer and probe binding sites and ranged from 10 7 to 10 1 c/rxn. The number of genome equivalents per reaction (Geq/rxn) was estimated by dividing c/rxn by six, reflecting the sixfold replication of the 5S‐16S‐23S rRNA operon in the P. salmonis genome (Nourdin‐Galindo et al, ).…”