Genome variability and gene content in chordopoxviruses: dependence on microsatellites.
To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites-simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution.
Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA. eneidao@uab.edu.
Eneida L
EL
Hatcher
Stanford Genome Technology Center, Stanford University, 855 California Ave, Palo Alto, CA 94304, USA. wangcl@stanford.edu.
Chunlin
C
Wang
Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA. elliotl@uab.edu.
Elliot J
EJ
Lefkowitz
D018147:Chordopoxvirinae / Q000235:genetics*; D018389:Codon, Nonsense; D019295:Computational Biology; D019143:Evolution, Molecular; D017353:Gene Deletion; D014644:Genetic Variation; D016679:Genome, Viral; D042822:Genomic Instability; D018895:Microsatellite Repeats
D018389:Codon, Nonsense