Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida

Abstract

Background: Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date.

Results: We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.

Conclusion: Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

Fig. 1

View of the salmonicida species section of the phylogenetic tree with proportional branch lengths. See Additional file 1 for the complete tree for all the aeromonads. Putative chromosome sequences were constructed for all the taxa and were compared based on their phylogenetic positions. The red alignments show identity between direct sequences while the gray ones show between inverted sequences. Only the subspecies of each A. salmonicida strain are indicated on the right. The geographic provenance of each taxon is indicated in brackets. Only bootstrap values below 100 are shown. The gradient from red to blue represents the ability of each taxon to grow at a mesophilic temperature (red) or at a strict psychrophilic one (blue)

Fig. 2

Growth curves at 37 °C (a) and 18 °C (b) for selected A. salmonicida subspecies. The growth curves were determined three times in independent experiments. The means of three replicates with standard error of the means are shown for each subspecies

Fig. 3

Distribution of the pan-genome on a phylogenetic tree for some key taxa. The phylogenetic tree was based on the tree found using the core genome. The green and black values indicate the number of genes acquired and lost, respectively, for the specific branch using the parsimonious Dollo model. The branch lengths represent the total number of genes acquired or lost. The three functional categories for which genes are the most affected for branches 1 and 2 are indicated. For more details on the analysis of the functional categories see Additional file 1. For A. salmonicida subsp. salmonicida the strain used was 01-B526

Fig. 4

Relative abundance of ISs in A. salmonicida subspecies. The distribution of 8 ISs significantly found in the mesophilic isolates (a) and 6 in the psychrophilic isolates (b) have been determined in a representative set of sequenced A. salmonicida isolates

Fig. 5

Venn diagram representing the genes under positive selection in the mesophilic, psychrophilic, and intermediate lineages