Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome
| Autor: | Pin Cui, Yasuko Ishida, Alfred L. Roca, Matthew C. Siracusa, Hanna Vielgrader, Kyriakos Tsangaras, Nikolas Nikolaidis, Kristofer M. Helgen, Alex D. Greenwood |
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| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Evolutionary Genetics
Models Molecular lcsh:Medicine Wildlife Genome Conserved sequence Retrovirus Proviruses Natural Selection lcsh:Science Genome Evolution Conserved Sequence Genetics 0303 health sciences Multidisciplinary 030302 biochemistry & molecular biology Nucleic Acid Hybridization Genomics Phascolarctidae Research Article Protein Binding Evolutionary Processes Animal Types Virus Integration Sequence alignment Genome Viral Biology Microbiology Viral Evolution DNA sequencing Evolution Molecular 03 medical and health sciences Phascolarctos cinereus Virology biology.animal Animals Codon 030304 developmental biology Evolutionary Biology Binding Sites Polymorphism Genetic lcsh:R Terminal Repeat Sequences Biology and Life Sciences Computational Biology biology.organism_classification Organismal Evolution Protein Structure Tertiary Retroviridae Microbial Evolution Koala retrovirus Veterinary Science lcsh:Q Sequence Alignment Transcription Factors |
| Zdroj: | PLoS ONE, Vol 9, Iss 4, p e95633 (2014) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin. |
| Databáze: | OpenAIRE |
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