In this study, the factors driving genome-wide patterns of codon usages in 
Lawsonia intracellularis genome are determined. For genes on the chromosome of 
the bacterium, it is found that the most important source of variation results 
from strand-specific mutational biases. A lesser trend of variation is 
attributable to genes that are presumed as horizontally transferred. These 
putative alien genes are unusually GC richer than the other genes, whereas 
horizontally transferred genes have been observed to be AT rich in bacteria with 
medium and relatively low G + C contents. Hydropathy of encoded protein and 
expression level are also found to influence codon usage. Therefore, codon usage 
in L. intracellularis chromosome is the result of a complex balance among the 
different mutational and selectional factors. When analyzing genes in the 
largest plasmid, for the first time it is found that the strand-specific 
mutational biases are responsible for the primary variation of codon usages in 
plasmid. Genes, particularly highly expressed genes of this plasmid, are mainly 
located on the leading strands and this supposed to be the effects exerted by 
replicational-transcriptional selection. These facts suggest that this plasmid 
adopts the similar mechanism of replication as the chromosome in L. 
intracellularis. Common characters among the 10 bacteria in whose genomes the 
strand-specific mutational biases are the primary source of variation of codon 
usage are also investigated. For example, it is found that genes dnaT and fis 
that are involved in DNA replication initiation and re-initiation pathways are 
absent in all of the 10 bacteria.