title: Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.
abstract: Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.
authors.affiliation: Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Liurong
authors.initials: L
authors.lastname: Fang
authors.forename: Mao
authors.initials: M
authors.lastname: Li
authors.forename: Sha
authors.initials: S
authors.lastname: Li
authors.forename: Shaohua
authors.initials: S
authors.lastname: Guo
authors.forename: Rui
authors.initials: R
authors.lastname: Luo
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Feng
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.forename: Zhemin
authors.initials: Z
authors.lastname: Zhou
authors.forename: Guoqing
authors.initials: G
authors.lastname: Shao
authors.forename: Huanchun
authors.initials: H
authors.lastname: Chen
authors.forename: Shaobo
authors.initials: S
authors.lastname: Xiao
mesh_terms: D017124:Conserved Sequence; D019143:Evolution, Molecular; D005787:Gene Frequency; D005798:Genes, Bacterial; D020043:Genes, Essential; D049810:Genetic Speciation; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D009174:Mycoplasma / Q000235:genetics*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S