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

TY - JOUR

T1 - Introducing the bacterial 'chromid'

T2 - not a chromosome, not a plasmid

AU - Harrison, Peter W.

AU - Lower, Ryan P. J.

AU - Kim, Nayoung K. D.

AU - Young, J. Peter W.

N1 - Although tagged as an "Opinion", this article proposes a novel concept based on comprehensive original bioinformatics research that is reported for the first time in this article and made up a significant part of the first author's PhD thesis.

PY - 2010/4

Y1 - 2010/4

N2 - 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.

AB - 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.

KW - UNIQUE CIRCULAR CHROMOSOMES

KW - SYNONYMOUS CODON USAGE

KW - VIBRIO-CHOLERAE

KW - SINORHIZOBIUM-MELILOTI

KW - GENOME

KW - GENES

KW - SELECTION

KW - SEQUENCE

KW - ORGANIZATION

KW - EVOLUTION

UR - http://www.scopus.com/inward/record.url?scp=77950802816&partnerID=8YFLogxK

U2 - 10.1016/j.tim.2009.12.010

DO - 10.1016/j.tim.2009.12.010

M3 - Article

SN - 0966-842X

VL - 18

SP - 141

EP - 148

JO - Trends in microbiology

JF - Trends in microbiology

IS - 4

ER -