Compositional discordance between prokaryotic plasmids and host chromosomes.docVIP

BMC Genomics BioMedCentral Research article Open Access Compositional discordance between prokaryotic plasmids and host chromosomes Mark WJ van Passel1, Aldert Bart1, Angela CM Luyf2, Antoine HC van Kampen2 and Arie van der Ende*1 Address: 1Academic Medical Center, Department of Medical Microbiology, Amsterdam, The Netherlands and 2Academic Medical Center, Bioinformatics Laboratory, Amsterdam, The Netherlands Email: Mark WJ van Passel - m.w.vanpassel@amc.uva.nl; Aldert Bart - a.bart@amc.uva.nl; Angela CM Luyf - a.c.luyf@amc.uva.nl; Antoine HC van Kampen - a.h.vankampen@amc.uva.nl; Arie van der Ende* - a.vanderende@amc.uva.nl * Corresponding author Published: 15 February 2006 Received: 04 July 2005 Accepted: 15 February 2006 BMC Genomics 2006, 7:26 doi:10.1186/1471-2164-7-26 This article is available from: /1471-2164/7/26 ? 2006 van Passel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Most plasmids depend on the host replication machinery and possess partitioning genes. These properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. Hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. However, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, suggesting dinucleotide composition dissimilarity between plasmid and host genome. We compared the dinucleotide composition of a large collection of plasmids with that of their host genomes to shed more light on this enigma. Results: The dinucleotide frequen