Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison
Abstract The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic ana...
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ftciteseerx:oai:CiteSeerX.psu:10.1.1.1081.1603 2023-05-15T16:05:19+02:00 Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison Comp Funct Aimée J Luers Sandra D Adams John V Smalley James J Campanella Montclair James J Campanella The Pennsylvania State University CiteSeerX Archives 2005 application/pdf http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1081.1603 http://downloads.hindawi.com/journals/ijg/2005/501927.pdf en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1081.1603 http://downloads.hindawi.com/journals/ijg/2005/501927.pdf Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://downloads.hindawi.com/journals/ijg/2005/501927.pdf text 2005 ftciteseerx 2020-05-03T00:24:38Z Abstract The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus. Text Elephant Seal Southern Elephant Seal Unknown |
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description |
Abstract The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus. |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Comp Funct Aimée J Luers Sandra D Adams John V Smalley James J Campanella Montclair James J Campanella |
spellingShingle |
Comp Funct Aimée J Luers Sandra D Adams John V Smalley James J Campanella Montclair James J Campanella Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
author_facet |
Comp Funct Aimée J Luers Sandra D Adams John V Smalley James J Campanella Montclair James J Campanella |
author_sort |
Comp Funct |
title |
Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
title_short |
Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
title_full |
Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
title_fullStr |
Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
title_full_unstemmed |
Comparative and Functional Genomics A phylogenomic study of the genus Alphavirus employing whole genome comparison |
title_sort |
comparative and functional genomics a phylogenomic study of the genus alphavirus employing whole genome comparison |
publishDate |
2005 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1081.1603 http://downloads.hindawi.com/journals/ijg/2005/501927.pdf |
genre |
Elephant Seal Southern Elephant Seal |
genre_facet |
Elephant Seal Southern Elephant Seal |
op_source |
http://downloads.hindawi.com/journals/ijg/2005/501927.pdf |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1081.1603 http://downloads.hindawi.com/journals/ijg/2005/501927.pdf |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
_version_ |
1766401217775271936 |