Genome-wide reexamination of endogenous retroviruses in Rattus norvegicus.
Endogenous retroviruses (ERVs) are remnants of retroviral infections that are present in a large number of vertebrate genomes. Based on the proposal that the rat could act as a reservoir of retroviruses, rat ERVs were analysed in silico using a whole-genome approach. To enrich the detected ERV groups, we applied an upgraded approach based on the hidden Markov model. We found 2637 elements that were classified into the following groups: 9 groups of Class I; 15 of Class II, 7 of them previously described; 1 of Class III; and 3 groups whose classification was unclear but were distantly related to Class I. Sixteen ERV groups seemed to be specific to rat. The high number of rat-specific groups might be related to the contact of rats with retroviruses and their role as a reservoir. In addition, the env gene of the more extended groups seemed to be undetectable.
Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 644 Postakutxa, E-48080 Bilbao, Spain.
Koldo
K
Garcia-Etxebarria
Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 644 Postakutxa, E-48080 Bilbao, Spain. Electronic address: begonamarina.jugo@ehu.es.
Begoña M
BM
Jugo
D000818:Animals; D002874:Chromosome Mapping; D019295:Computational Biology; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D008322:Mammals; D051379:Mice; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D020079:Terminal Repeat Sequences
Colonisation; Endogenous retroviruses; Genome; Rat; Reservoir