Introducing the bacterial 'chromid': not a chromosome, not a plasmid.

In addition to the main chromosome, approximately one in ten bacterial genomes have a 'second chromosome' or 'megaplasmid'. Here, we propose that these represent a single class of elements that have a distinct and consistent set of properties, and suggest the term 'chromid' to distinguish them from both chromosomes and plasmids. Chromids carry some core genes, and their nucleotide composition and codon usage are very similar to those of the chromosomes they are associated with. By contrast, they have plasmid replication and partitioning systems and the majority of their genes confer accessory functions. Chromids seem particularly rich in genus-specific genes and appear to be 'reinvented' at the origin of a new genus.

[1]  R. Zuerner,et al.  Comparison of genetic maps for two Leptospira interrogans serovars provides evidence for two chromosomes and intraspecies heterogeneity , 1993, Journal of bacteriology.

[2]  G. Perrière,et al.  The source of laterally transferred genes in bacterial genomes , 2003, Genome Biology.

[3]  G. Perrière,et al.  Use and misuse of correspondence analysis in codon usage studies. , 2002, Nucleic acids research.

[4]  J. Young,et al.  Genome sequencing: The ABC of symbiosis , 2001, Nature.

[5]  Masaru Tomita,et al.  A problem in multivariate analysis of codon usage data and a possible solution , 2005, FEBS letters.

[6]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[7]  H. Mori,et al.  The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. , 2008, Methods in molecular biology.

[8]  M. Gouy,et al.  Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. , 1980, Nucleic acids research.

[9]  Eva M. Top,et al.  Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes , 2008, Nucleic acids research.

[10]  S. Karlin,et al.  Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Y. Yamaichi,et al.  Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species , 1999, Molecular microbiology.

[12]  D. Kahn,et al.  Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. , 2004, Molecular plant-microbe interactions : MPMI.

[13]  Kim Wong,et al.  The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[14]  L. Karayan,et al.  Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome , 1993, Journal of bacteriology.

[15]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[16]  M. Riley,et al.  Organization of the bacterial chromosome , 1990, Microbiological reviews.

[17]  J. Kaper,et al.  The Vibrio cholerae genome contains two unique circular chromosomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  H. Ochman.  Bacterial Evolution: Chromosome Arithmetic and Geometry , 2002, Current Biology.

[19]  M. Kocur,et al.  Trends in microbiology , 1992, World journal of microbiology & biotechnology.

[20]  S. Aiyar,et al.  rRNA Promoter Activity in the Fast-Growing Bacterium Vibrio natriegens , 2002, Journal of bacteriology.

[21]  Eduardo P C Rocha,et al.  Base composition bias might result from competition for metabolic resources. , 2002, Trends in genetics : TIG.

[22]  A. Pühler,et al.  Direct selection for curing and deletion of Rhizobium plasmids using transposons carrying the Bacillus subtilis sacB gene. , 1989, Gene.

[23]  D. Lynn,et al.  Synonymous codon usage is subject to selection in thermophilic bacteria. , 2002, Nucleic acids research.

[24]  S Kaplan,et al.  Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes , 1989, Journal of bacteriology.

[25]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Eric D Brown,et al.  Are essential genes really essential? , 2009, Trends in microbiology.

[27]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[28]  W. F. Fricke,et al.  The Genome Organization of Ralstonia eutropha Strain H16 and Related Species of the Burkholderiaceae , 2008, Journal of Molecular Microbiology and Biotechnology.

[29]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[30]  Angela C. M. Luyf,et al.  Compositional discordance between prokaryotic plasmids and host chromosomes , 2006, BMC Genomics.

[31]  Guillermo Dávila,et al.  Natural genomic design in Sinorhizobium meliloti: novel genomic architectures. , 2003, Genome research.

[32]  Luke E. Ulrich,et al.  Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility , 2006, Proceedings of the National Academy of Sciences.

[33]  R. B. Jensen,et al.  The two chromosomes of Vibrio cholerae are initiated at different time points in the cell cycle , 2007, The EMBO journal.

[34]  P. Sharp,et al.  Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. , 1986, Nucleic acids research.

[35]  Steven C. Slater,et al.  Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria , 2009, Journal of bacteriology.

[36]  Kim Wong,et al.  Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids , 2002, Functional & Integrative Genomics.

[37]  J. Mekalanos,et al.  Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  S. Salzberg,et al.  DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae , 2000, Nature.

[39]  J. Paillisson,et al.  Presence of two independent chromosomes in the Brucella melitensis 16M genome , 1993, Journal of bacteriology.

[40]  Larry J. Forney,et al.  Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.