dnaJ is a useful phylogenetic marker for alphaproteobacteria

Area of Science:

• Microbiology
• Molecular Biology
• Bioinformatics

Background:

• Bacterial phylogeny traditionally relied on 16S rRNA gene sequencing.
• Multilocus sequence analysis (MLSA) has emerged as a more robust method for inferring evolutionary relationships.
• The suitability of alternative genes for phylogenetic studies requires ongoing investigation.

Purpose of the Study:

• To evaluate the dnaJ chaperone gene as a phylogenetic marker for Alphaproteobacteria.
• To compare dnaJ-based phylogenies with those derived from 16S rRNA gene sequences and MLSA.
• To assess the accuracy of dnaJ for bacterial identification at different taxonomic levels.

Main Methods:

• Sequence analysis of the dnaJ gene in various bacterial taxa.
• Phylogenetic tree construction using dnaJ and 16S rRNA gene sequences.
• Comparison of dnaJ phylogenies with established relationships and MLSA data.
• Analysis of G+C and G+C3s content to assess horizontal gene transfer potential.

Main Results:

• DnaJ-based phylogenies accurately reflected established relationships within Proteobacteria and Alphaproteobacteria.
• At the Alphaproteobacteria level, dnaJ phylogenies showed greater consistency with MLSA than 16S rRNA gene phylogenies.
• For the genus Mesorhizobium, dnaJ analysis produced a tree topology similar to MLSA, unlike 16S rRNA gene analysis.
• Both 16S rRNA and dnaJ analyses led to consistent species identification for chickpea isolates.

Conclusions:

• The dnaJ gene is a valuable phylogenetic marker, particularly for the class Alphaproteobacteria.
• DnaJ analysis provides a more accurate reflection of evolutionary history in Alphaproteobacteria compared to 16S rRNA gene sequencing.
• The dnaJ gene's phylogenetic signal is consistent with multilocus approaches, enhancing its reliability for bacterial classification.