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In Silico Biology 7, 0039 (2007); ©2007, Bioinformation Systems e.V.  

Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation

Gargi Sen1, Saubashya Sur1, Debadin Bose1, Uttam Mondal2, Teal Furnholm3, Asim Bothra2, Louis Tisa3 and Arnab Sen1,3*

1 DBT-Bioinformatics facility, Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India
2 Bioinformatics Cheminformatics Laboratory, Department of Chemistry, Raiganj University College, Raiganj, India
3 Department of Microbiology, University of New Hampshire, Durham NH, USA

Edited by H. Michael; received April 20, 2007; revised August 08, 2007; accepted August 09, 2007; published August 21, 2007


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.

Keywords: codon usage, codon adaptation index, correspondence analysis, pathogenicity, Xanthomonas