title: Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum.
abstract: The increasing number of genome sequences of archaea and bacteria show their adaptation to different environmental conditions at the genomic level. Aeropyrum spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were a small genome size, a high GC content, and a large portion of orthologous genes (86 to 88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the entire-genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A. pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini CRISPR showed significant matches with protospacers of the two proviruses infecting A. pernix, indicating that A. camini interacted with viruses closely related to APSV1 and APOV1. Furthermore, a significant fraction of the nonorthologous genes (41 to 45%) were proviral genes or ORFans probably originating from viruses. Although the genomes of A. camini and A. pernix were conserved, we observed nonsynteny that was attributed primarily to virus-related elements. Our findings indicated that the genomic diversification of Aeropyrum spp. is substantially caused by viruses.
authors.affiliation: Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Daifuku
authors.forename: Takashi
authors.initials: T
authors.lastname: Yoshida
authors.forename: Takayuki
authors.initials: T
authors.lastname: Kitamura
authors.forename: Satoshi
authors.initials: S
authors.lastname: Kawaichi
authors.forename: Takahiro
authors.initials: T
authors.lastname: Inoue
authors.forename: Keigo
authors.initials: K
authors.lastname: Nomura
authors.forename: Yui
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Sotaro
authors.initials: S
authors.lastname: Kuno
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Sako
mesh_terms: D041522:Aeropyrum / Q000235:genetics* / Q000302:isolation & purification / Q000821:virology*; D001482:Base Composition; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D020745:Genome, Archaeal; D060086:Hydrothermal Vents / Q000382:microbiology; D008969:Molecular Sequence Data; D011533:Proviruses / Q000235:genetics*; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D019641:DNA, Archaeal