In-silico Comparison of Predicted 16S rRNA Secondary Structure in Strains of Xanthomonas axonopodis pv. Punicae: A Preliminary Note

Abstract

This study evaluates the predicted secondary structure and structural alignment of 16S rRNA sequences from two previously reported strains of Xanthomonas axonopodis pv. punicae, designated Xa1 and Xa2, together with selected representative Xanthomonas sequences. The analysis was performed using publicly available in silico RNA structure-prediction and alignment tools. The 16S rRNA sequence of each strain was compared with the NCBI reference sequence NR_026317.1, and RNA folding patterns were examined to assess possible structural differences between the strains. The predicted thermodynamic ensemble free energy (dG) was -259.03 kcal/mol for Xa1 and -249.87 kcal/mol for Xa2, indicating that Xa1 had a comparatively more thermodynamically stable predicted structure. The dG values of the other Xanthomonas sequences also varied with changes in predicted RNA structure. Foldalign-based structural comparison suggested that Xa2 had several regions of similarity, insertion/deletion and structurally stable motifs, indicating structural divergence relative to the reference sequence, whereas Xa1 showed a more contiguous alignment with regions of shared base pairs and motifs. The Xa2 result differed from the other Xanthomonas alignments. These observations indicate that variation in 16S rRNA sequence composition may be associated with differences in predicted folding patterns among closely related strains. The findings support RNA secondary-structure prediction as a complementary approach for examining strain-level variation in bacterial 16S rRNA. However, because the results are based solely on computational prediction, further experimental validation and broader comparative analysis are required.