Direct evidence of recombination in the recA gene of Aeromonas bestiarum

Abstract

Two hundred and twenty-one strains representative of all Aeromonas species were characterized using the recA gene sequence, assessing its potential as a molecular marker for the genus Aeromonas. The inter-species distance values obtained demonstrated that recA has a high discriminatory power. Phylogenetic analysis, based on full-length gene nucleotide sequences, revealed a robust topology with clearly separated clusters for each species. The maximum likelihood tree showed the Aeromonas bestiarum strains in a well-defined cluster, containing a subset of four strains of different geographical origins in a deep internal branch. Data analysis provided strong evidence of recombination at the end of the recA sequences in these four strains. Intergenomic recombination corresponding to partial regions of the two adjacent genes recA and recX (248 bp) was identified between A. bestiarum (major parent) and Aeromonas eucrenophila (minor parent). The low number of recombinant strains detected (1.8%) suggests that horizontal flow between recA sequences is relatively uncommon in this genus. Moreover, only a few nucleotide differences were detected among these fragments, indicating that recombination has occurred recently. Finally, we also determined if the recombinant fragment could have influenced the structure and basic functions of the RecA protein, comparing models reconstructed from the translated amino acid sequences of our A. bestiarum strains with known Escherichia coli RecA structures.

Genetic relatedness and novel sequence types of clinical Aeromonas dhakensis from Malaysia

“…For example, gyrB is better in splitting A. allosaccharophila from A. veronii while rpoD is better in splitting A. salmonicida from A. bestiarum [35]. Trees of gltA, ppsA, and recA could not separate some Aeromonas species from A. dhakensis, and this could possibly be due to recombination events or mutations as documented in previous studies [3,36,37]. Therefore, MLPA tree, which combines the capability of multiple genes to buffer against the effect of recombination in individual genes, is recommended [13,35].…”

Evolutionary Roots and Diversification of the Genus Aeromonas

“…Bacterial isolates and reference strains were obtained from several type culture collections, kindly supplied by other authors (Katri Berg, University of Helsinki, Helsinki, Finlandia; Yogesh Shouche, Molecular Biology Laboratory, National Centre for Cell Science, Pune, India; Margarita Gomila, Universitat de les Illes Balears, Palma de Mallorca, Spain; M a José Figueras, Universitat Rovira i Virgili, Reus, Spain; Antonio Martínez-Murcia, Universidad de Alicante, Spain) or from samplings of freshwater and food carried out by our research group ( Miñana-Galbis et al, 2002 ). Species-level identification of these isolates were performed in previous studies by phenotypical and/or molecular approaches ( Miñana-Galbis et al, 2002 ; Miñana-Galbis et al, 2009 ; Farfán et al, 2010 ; Fusté et al, 2012 ; Sanglas et al, 2016 ). Bacterial culture conditions and genomic DNA extraction were performed as described previously ( Farfán et al, 2010 ).…”

“…Bacterial culture conditions and genomic DNA extraction were performed as described previously ( Farfán et al, 2010 ). Two housekeeping genes ( mdh and recA ) were chosen for the analysis; for each strain, the full-length sequences for both genes were obtained, using methods previously reported ( Farfán et al, 2010 ; Sanglas, 2015 ; Sanglas et al, 2016 ). The sequences determined in this paper were deposited in the GenBank 1 .…”

Wolbachia strains in cryptic species of the Anastrepha fraterculus complex (Diptera, Tephritidae) along the Neotropical Region

“…In the phylogenetic analyses that follow the putative recombinant sequences were not included since the Maximum Likelihood (ML) methodology requires sequences with the same evolutionary history [42,64]. Phylogenetic inference based on the concatenated set of the five MLST genes (Fig.…”