Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region
| dc.contributor.author | Carulei, Olivia | |
| dc.contributor.author | Douglass, Nicola | |
| dc.contributor.author | Williamson, Anna-Lise | |
| dc.date.accessioned | 2017-12-15T07:02:32Z | |
| dc.date.available | 2017-12-15T07:02:32Z | |
| dc.date.issued | 2017-12-06 | |
| dc.date.updated | 2017-12-10T04:58:09Z | |
| dc.description.abstract | Background: Avian poxviruses are important pathogens of both wild and domestic birds. To date, seven isolates from subclades A and B and one from proposed subclade E, have had their genomes completely sequenced. The genomes of these isolates have been shown to exhibit typical poxvirus genome characteristics with conserved central regions and more variable terminal regions. Infection with avian poxviruses (APVs) has been reported in three species of captive flamingo, as well as a free-living, lesser flamingo at Kamfers dam, near Kimberley, South Africa. This study was undertaken to further characterise this virus which may have long term effects on this important and vulnerable, breeding population. Results: Gene content and synteny as well as percentage identities between conserved orthologues was compared between Flamingopox virus (FGPV) and the other sequenced APV genomes. Dotplot comparisons revealed major differences in central regions that have been thought to be conserved. Further analysis revealed five regions of difference, of differing lengths, spread across the central, conserved regions of the various genomes. Although individual gene identities at the nucleotide level did not vary greatly, gene content and synteny between isolates/species at these identified regions were more divergent than expected. Conclusion: Basic comparative genomics revealed the expected similarities in genome architecture but an in depth, comparative, analysis showed all avian poxvirus genomes to differ from other poxvirus genomes in fundamental and unexpected ways. The reasons for these large genomic rearrangements in regions of the genome that were thought to be relatively conserved are yet to be elucidated. Sequencing and analysis of further avian poxvirus genomes will help characterise this complex genus of poxviruses. | |
| dc.identifier.apacitation | Carulei, O., Douglass, N., & Williamson, A. (2017). Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region. <i>BMC Genomics</i>, http://hdl.handle.net/11427/26697 | en_ZA |
| dc.identifier.chicagocitation | Carulei, Olivia, Nicola Douglass, and Anna-Lise Williamson "Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region." <i>BMC Genomics</i> (2017) http://hdl.handle.net/11427/26697 | en_ZA |
| dc.identifier.citation | Carulei, O., Douglass, N., & Williamson, A. L. (2017). Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region. BMC genomics, 18(1), 947. | |
| dc.identifier.ris | TY - Journal Article AU - Carulei, Olivia AU - Douglass, Nicola AU - Williamson, Anna-Lise AB - Background: Avian poxviruses are important pathogens of both wild and domestic birds. To date, seven isolates from subclades A and B and one from proposed subclade E, have had their genomes completely sequenced. The genomes of these isolates have been shown to exhibit typical poxvirus genome characteristics with conserved central regions and more variable terminal regions. Infection with avian poxviruses (APVs) has been reported in three species of captive flamingo, as well as a free-living, lesser flamingo at Kamfers dam, near Kimberley, South Africa. This study was undertaken to further characterise this virus which may have long term effects on this important and vulnerable, breeding population. Results: Gene content and synteny as well as percentage identities between conserved orthologues was compared between Flamingopox virus (FGPV) and the other sequenced APV genomes. Dotplot comparisons revealed major differences in central regions that have been thought to be conserved. Further analysis revealed five regions of difference, of differing lengths, spread across the central, conserved regions of the various genomes. Although individual gene identities at the nucleotide level did not vary greatly, gene content and synteny between isolates/species at these identified regions were more divergent than expected. Conclusion: Basic comparative genomics revealed the expected similarities in genome architecture but an in depth, comparative, analysis showed all avian poxvirus genomes to differ from other poxvirus genomes in fundamental and unexpected ways. The reasons for these large genomic rearrangements in regions of the genome that were thought to be relatively conserved are yet to be elucidated. Sequencing and analysis of further avian poxvirus genomes will help characterise this complex genus of poxviruses. DA - 2017-12-06 DB - OpenUCT DO - 10.1186/s12864-017-4315-0 DP - University of Cape Town J1 - BMC Genomics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2017 T1 - Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region TI - Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region UR - http://hdl.handle.net/11427/26697 ER - | en_ZA |
| dc.identifier.uri | http://dx.doi.org/10.1186/s12864-017-4315-0 | |
| dc.identifier.uri | http://hdl.handle.net/11427/26697 | |
| dc.identifier.vancouvercitation | Carulei O, Douglass N, Williamson A. Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region. BMC Genomics. 2017; http://hdl.handle.net/11427/26697. | en_ZA |
| dc.language.iso | en | |
| dc.publisher | BioMed Central | |
| dc.publisher.department | Division of Virology | en_ZA |
| dc.publisher.faculty | Faculty of Health Sciences | en_ZA |
| dc.publisher.institution | University of Cape Town | |
| dc.rights.holder | The Author(s). | |
| dc.source | BMC Genomics | |
| dc.source.uri | https://bmcgenomics.biomedcentral.com/ | |
| dc.subject.other | Poxvirus | |
| dc.subject.other | Avipoxvirus | |
| dc.subject.other | Flamingopox | |
| dc.subject.other | Genome sequence | |
| dc.title | Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region | |
| dc.type | Journal Article | |
| uct.type.filetype | Text | |
| uct.type.filetype | Image |