Affiliations: DBT-Bioinformatics facility, Molecular Genetics
Laboratory, Department of Botany, University of North Bengal, Siliguri 734013,
India | Bioinformatics Cheminformatics Laboratory, Department
of Chemistry, Raiganj University College, Raiganj, India | Department of Microbiology, University of New
Hampshire, Durham NH, USA
Abstract: Members of the genus Xanthomonas are significant
phytopathogens, which cause diseases in several economically important crops
including rice, canola, tomato, citrus, etc. We have analyzed the genomes of
six recently sequenced Xanthomonas strains for their synonymous codon
usage patterns for all of protein coding genes and specific genes associated
with pathogenesis, and determined the predicted highly expressed (PHX) genes by
the use of the codon adaptation index (CAI). Our results show considerable
heterogeneity among the genes of these moderately G+C rich
genomes. Most of the genes were moderate to highly biased in their codon usage.
However, unlike ribosomal protein genes, which were governed by translational
selection, those genes associated with pathogenesis (GAP) were affected by
mutational pressure and were predicted to have moderate to low expression
levels. Only two out of 339 GAP genes were in the PHX category. PHX genes
present in clusters of orthologous groups of proteins (COGs) were identified.
Genes in the plasmids present in two strains showed moderate to low expression
level and only a couple of genes featured in the PHX list. Common genes present
in the top-20 PHX gene-list were identified and their possible functions are
discussed. Correspondence analysis showed that genes are highly confined to a
core in the plot.