Identification of lateral gene in the genomic DNA sequence, by using the G+C content at the third position of synonymous codons of orthologous genes as an index

Abstract

All open reading frames (ORFs) of 6 Archaebacterial and 17 Eubacterial species showed a strong positive correlation between the G+C content (GC content) of the genomic DNA sequences and the G+C content of the third position of the codons (GC3 content). Among them, 1217 pairs of genes that are orthologous between Pyrococcus horikoshii OT3 (Ph) and Pyrococcus abyssi (Pa) were identified. The codons of each pair of orthologous genes were classified into three categories, identical codons coding for the same amino acid (IC), different codon coding for the different amino acids (DC) and synonymous codons coding for the same amino acids (IA). In a comparison of the GC3 content of these three types in all orthologous genes between Ph and Pa, the GC3 content of IA (GC3 content of synonymous codons) deviated the most from the expected value for the GC content of the genome sequences used in this analysis. Therefore the GC3 content of synonymous codon was suggested to be an index that would be able to distinguish a lateral gene from the orthologous genes of the genomic DNA sequence. By analysis of the GC3 content of synonymous codons, two remarkable regions were found in the genome sequence of Ph. In one region between 300 Kbp and 420 Kbp, the genes have a higher GC3 content in the synonymous codon, and in the other between 1, 320 Kbp and 1, 400 Kbp, the genes have a lower GC3 content in the synonymous codons. In the former region, twelve of sixteen orthologous genes were homologous to genes of Eubacteria or Archaebacteria. Especially, four orthologous genes showed homology to genes related to synthesis of the cell wall or lipopolysaccharides from Streptococcus. These four genes would be suggested to be lateral genes and to represent a lateral region from Eubacterial species. In the latter region, eight out of thirteen orthologous genes were homologous to genes of Archaebacteria or Eukarya. Six of these eight orthologous genes show homology to the genes related to the function of translation. These genes would be indicated as the stable genes in the progress of evolution, after the divergence between Pyrococcus horikoshii OT3 and Pyrococcus abyssi.