title: Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group.
abstract: BACKGROUND
  Prokaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell. Many bacterial strains contain multiple plasmids, but the relationships between bacterial plasmids and chromosomes are unclear. We focused on plasmids from the Bacillus cereus group because most strains contain several plasmids.
  
  
  RESULTS
  We collected the genome sequences of 104 plasmids and 20 chromosomes from B. cereus group strains, and we studied the relationships between plasmids and chromosomes by focusing on the pan-genomes of these plasmids and chromosomes. In terms of basic features (base composition and codon usage), the genes on plasmids were more similar to the chromosomal variable genes (distributed genes and unique genes) than to the chromosomal core genes. Although all the functional categories of the chromosomal genes were exhibited by the plasmid genes, the proportions of each category differed between these two gene sets. The 598 gene families shared between chromosomes and plasmids displayed a uniform distribution between the two groups. A phylogenetic analysis of the shared genes, including the chromosomal core gene set, indicated that gene exchange events between plasmids and chromosomes occurred frequently during the evolutionary histories of the strains and species in this group. Moreover, the shared genes between plasmids and chromosomes usually had different promoter and terminator sequences, suggesting that they are regulated by different elements at the transcriptional level.
  
  
  CONCLUSIONS
  We speculate that for the entire B. cereus group, adaptive genes are preserved on both plasmids and chromosomes; however, in a single cell, homologous genes on plasmids and the chromosome are controlled by different regulators to reduce the burden of maintaining redundant genes.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. jszheng@mail.hzau.edu.cn.
authors.forename: Jinshui
authors.initials: J
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. dearyu.yu@163.com.
authors.forename: Ziyu
authors.initials: Z
authors.lastname: Guan
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. csy86@webmail.hzau.edu.cn.
authors.forename: Shiyun
authors.initials: S
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. donghaipeng@mail.hzau.edu.cn.
authors.forename: Donghai
authors.initials: D
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. ruanlifang@mail.hzau.edu.cn.
authors.forename: Lifang
authors.initials: L
authors.lastname: Ruan
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. daohongjiang@mail.hzau.edu.cn.
authors.forename: Daohong
authors.initials: D
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. m98sun@mail.hzau.edu.cn.
authors.forename: Ming
authors.initials: M
authors.lastname: Sun
mesh_terms: D001409:Bacillus cereus / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D005075:Biological Evolution; D002876:Chromosomes, Bacterial / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D030541:Databases, Genetic; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins