TY - JOUR

T1 - Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

A1 - Bohlin,Jon

A1 - van Passel,Mark W. J.

A1 - Snipen,Lars

A1 - Kristoffersen,Anja B.

A1 - Ussery,David

A1 - Hardy,Simon P.

AU - Bohlin,Jon

AU - van Passel,Mark W. J.

AU - Snipen,Lars

AU - Kristoffersen,Anja B.

AU - Ussery,David

AU - Hardy,Simon P.

PB - BioMed Central Ltd.

PY - 2012

Y1 - 2012

N2 - <p><strong>Background: </strong>We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. <br/> <strong>Results:</strong> Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes &gt; GI &gt; phage &gt; plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. <br/> <strong>Conclusions: </strong>We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.</p>

AB - <p><strong>Background: </strong>We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. <br/> <strong>Results:</strong> Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes &gt; GI &gt; phage &gt; plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. <br/> <strong>Conclusions: </strong>We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.</p>

KW - BIOTECHNOLOGY

KW - GENETICS

KW - USAGE PATTERNS

KW - SEQUENCES

KW - PROKARYOTES

KW - COMMUNICATION

KW - REDUCTION

KW - DIVERSITY

KW - ANCESTOR

UR - http://www.biomedcentral.com/1471-2164/13/66

U2 - 10.1186/1471-2164-13-66

DO - 10.1186/1471-2164-13-66

JO - B M C Genomics

JF - B M C Genomics

SN - 1471-2164

IS - 66

VL - 13

ER -