Selected article for: "capsid protein fold and protein fold"

Author: Nasir, Arshan; Caetano-Anollés, Gustavo
Title: A phylogenomic data-driven exploration of viral origins and evolution
  • Document date: 2015_9_25
  • ID: 49360l2a_38
    Snippet: We evaluated ToP phylogeny by comparing it against ICTV and structure-based classifications. ToP recovered some well-known relationships. For example, the genera Flavivirus (Flaviviridae) and Alphavirus (Togaviridae) were grouped together, suggesting their close evolutionary association (66% BS). In fact, alphaviruses were initially classified by the ICTV under Flaviviridae but were later assigned their own genera in Togaviridae. Both viral famil.....
    Document: We evaluated ToP phylogeny by comparing it against ICTV and structure-based classifications. ToP recovered some well-known relationships. For example, the genera Flavivirus (Flaviviridae) and Alphavirus (Togaviridae) were grouped together, suggesting their close evolutionary association (66% BS). In fact, alphaviruses were initially classified by the ICTV under Flaviviridae but were later assigned their own genera in Togaviridae. Both viral families show striking similarities in virion architecture (enveloped and spherical) and genome replication strategies (monopartite linear plus-ssRNA). Similarly, Polyomaviridae, Closteroviridae, Coronaviridae, and many others also formed individual monophyletic groups (indicated by asterisk in Fig. 7A ). Another largely unified group was that of filamentous dsDNA archaeoviruses (Rudiviridae and Lipothrixiviridae) that have been classified under the order "Ligamenvirales" (68) . Similarly, viral families in the "nucleocytoplasmic large DNA viruses" group (Poxviridae, Phycodnaviridae, Ascoviridae, Asfarviridae, Iridoviridae, and Mimiviridae) formed a paraphyletic group at the very derived positions. This group also included the recently discovered pandoraviruses (69) and pithoviruses (70) and the oddly placed bacteriophage (Myoviridae). The close grouping of all giant viruses supports the proposal of the viral order "Megavirales" (71) and a previous reconstruction (19) . However, herpesviruses and Caudovirales that share the common HK97 capsid protein fold did not form a single group (47) , but they were in close proximity (Fig. 7A ). In turn, Adenoviridae and Tectiviridae that belong to the PRD1/adenovirus-like lineage were closely clustered. Similarly, Totiviridae and some Reoviridae of the BTV-like lineage occupied basal positions. Some members of the picornavirus-like lineage (for example, Luteoviridae, Caliciviridae, and Picornaviridae) and retrotranscribing viruses also clustered together, but clear-cut structure-based viral lineages did not materialize in ToP. Other discrepancies also existed with regard to viral families defined by the ICTV that did not form unified groups. However, ICTV classifications are subject to revisions and do not always yield evolutionarily informative classifications. In light of these, ToP reconstructed from the abundance of conserved FSF domains present a "third" and global view of the evolutionary relationships of viruses, which adds deep lineage relationships to ICTV and structure-based classifications.

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