title: Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation.
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.
authors.affiliation: Department of Botany, University of North Bengal, Siliguri 734013, India.
authors.forename: Gargi
authors.initials: G
authors.lastname: Sen
authors.forename: Saubashya
authors.initials: S
authors.lastname: Sur
authors.forename: Debadin
authors.initials: D
authors.lastname: Bose
authors.forename: Uttam
authors.initials: U
authors.lastname: Mondal
authors.forename: Teal
authors.initials: T
authors.lastname: Furnholm
authors.forename: Asim
authors.initials: A
authors.lastname: Bothra
authors.forename: Louis
authors.initials: L
authors.lastname: Tisa
authors.forename: Arnab
authors.initials: A
authors.lastname: Sen
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics*; D003062:Codon / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000502:physiology*; D010935:Plant Diseases / Q000235:genetics; D012984:Software; D014974:Xanthomonas / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D003062:Codon