Adriaenssens, Evelien

Bamford, Dennis Henry

Breitbart, Mya

Dishaw, Larry J

Kropinki, Andrew

Leigh, Brittany A

Oksanen, Hanna Maarit

English

Helsingin yliopiston digitaalinen arkisto

https://helda.helsinki.fiTaxonomy proposal: One (1) new species, Pseudoalteromonasvirus Cr39582, in the genus Corticovirus, in the family CorticoviridaeLeigh, Brittany AInternational Committee on Taxonomy of Viruses (ICTV)2018Leigh , B A , Breitbart , M , Bamford , D H , Dishaw , L J , Adriaenssens , E , Kropinki , A &Oksanen , H M 2018 , Taxonomy proposal: One (1) new species, Pseudoalteromonas virusCr39582, in the genus Corticovirus, in the family Corticoviridae . in ICTV Online:International Committee on Taxonomy of Viruses (ICTV) . , 2018.123B , InternationalCommittee on Taxonomy of Viruses (ICTV) , pp. 2018.123B . <https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/prokaryote-official/8248>http://hdl.handle.net/10138/299804publishedVersionDownloaded from Helda, University of Helsinki institutional repository.This is an electronic reprint of the original article.This reprint may differ from the original in pagination and typographic detail.Please cite the original version.February 2018Page 1 of 3This Word module should be used for all taxonomic proposals.Please complete Part 1 and:either Part 3 for proposals to create new taxa or change existing taxaor Part 2 for proposals of a general nature.Submit the completed Word module, together with the accompanying Excelmodule named in Part 3, to the appropriate ICTV Subcommittee Chair.For guidance, see the notes written in blue, below, and the help notes in fileTaxonomic_Proposals_Help_2018.Part 1: TITLE, AUTHORS, etcCode assigned: 2018.123B (to be completed by ICTV officers)Short title: One (1) new species, Pseudoalteromonas virus Cr39582, in the genusCorticovirus, in the family Corticoviridae(e.g. “6 new species in the genus Zetavirus”)Author(s):Brittany A. Leigha,b*, Mya Breitbarta, Dennis H. Bamfordc, Larry J. Dishawb, EvelienAdriaenssensd, Andrew Kropinskie and Hanna M. OksanencaCollege of Marine Science, University of South Florida, St. Petersburg, Florida, USAbDepartment of Pediatrics, Children’s Research Institute, University of South Florida, St. Petersburg,Florida, USAcMolecular and Integrative Research Programme, Faculty of Biological and Environmental Sciences,University of Helsinki, Helsinki, FinlanddUniversity of Liverpool, UKeUniversity of Guelph, Canada*Current address: Department of Biological Sciences, Vanderbilt University, Nashville, TN, USACorresponding author with e-mail address:Hanna M. Oksanen, hanna.oksanen@helsinki.fiList the ICTV study group(s) that have seen this proposal:A list of study groups and contacts is provided athttp://www.ictvonline.org/subcommittees.asp . If indoubt, contact the appropriate subcommittee chair(there are six virus subcommittees: animal DNA andretroviruses, animal ssRNA-, animal ssRNA+, fungaland protist, plant, bacterial and archaeal)Bacterial and Archaeal VirusesSubcommitteeICTV Study Group comments (if any) and response of the proposer:Date first submitted to ICTV: June 6, 2018Date of this revision (if different to above):ICTV-EC comments and response of the proposer:February 2018Page 2 of 3Part 2: NON-STANDARDTemplate for any proposal regarding ICTV procedures, rules or policy, not involving the creation of newtaxonomy.Text of proposal:Part 3: PROPOSED TAXONOMYName of accompanying Excel module: 2018.123B.N.v1.Corticovirus_spThe taxonomic changes you are proposing should be presented on an accompanying Excel module,2017_TP_Template_Excel_module. Please enter the file name of the completed module in this box.Supporting material:additional material in support of this proposalPlease explain the reasons for the taxonomic changes you are proposing and provide evidence tosupport them. The following information should be provided, where relevant:∑ Species demarcation criteria: Explain how new species differ from others in the genus anddemonstrate that these differences meet the criteria previously established for demarcatingbetween species. If no criteria have previously been established, and if there will now be morethan one species in the genus, please state the demarcation criteria you are proposing.∑ Higher taxa:o There is no formal requirement to state demarcation criteria when proposing new generaor other higher taxa. However, a similar concept should apply in pursuit of a rational andconsistent virus taxonomy.o Please indicate the origin of names assigned to new taxa at genus level and above.o For each new genus a type species must be designated to represent it. Please explainyour choice.∑ Supporting evidence: The use of Figures and Tables is strongly recommended (note thatcopying from publications will require permission from the copyright holder). For phylogeneticanalysis, try to provide a tree where branch length is related to genetic distance.Species demarcation criteria: We propose to have 95% nucleotide sequence identity as the criterion fordemarcation of species in the genus Corticovirus. The proposed species Pseudoalteromonas virusCr39582 differs from the type species Pseudoalteromonas virus PM2 by ~15% at the nucleotide level asconfirmed by the full genome alignment by Mauve (Darling et al., 2010) and MUSCLE (Edgar, 2004)nucleotide alignments (Leigh et al., 2018). Pseudoalteromonas virus PM2 is currently the only species inthe genus Corticovirus, the family Corticoviridae (Oksanen, 2017).Supporting evidence: The Cr39582 and PM2 genomes are syntenous sharing sequence homologythroughout their genome lengths (Figures 1 and 2) (Leigh et al., 2018). The only exception is the Cr39582ORF (nucleotides 7982-9430) encoding for the putative spike protein which is not homologous with PM2spike protein P1. The nucleotide sequence identity between Cr39582 and PM2 spike encoding genes is~37%. Pairwise nucleotide identities between Cr39582 and PM2 in the 5’ and 3’ regions flanking the spikeprotein gene are ~91% and ~96%, respectively.February 2018Page 3 of 3Figure 1. Multiple genome alignment between the genomes of PM2 and Cr39582 (Mauve, Darling et al.,2010). Colored boxes indicate blocks of the genomes with high sequence identity, and regions lackinghomology appear as white.References:Darling AE, Mau B, Perna N. 2010. progressiveMauve: multiple genome alignment with gene gain,loss and rearrangement. PLoS One 5:e11147Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and highthroughput. Nucleic Acids Res. 32: 1792-1797.Leigh BA, Breitbart M, Oksanen HM, Bamford DH, Dishaw LJ. 2018. Genome sequence of PM2-likephage Cr39582, induced from a Pseudoalteromonas sp. isolated from the gut of Ciona robusta.Genome Announc. 6:e00368-18.Oksanen HM, ICTV Report Consortium. 2017. ICTV Virus Taxonomy Profile: Corticoviridae. J GenVirol. 98:888-889.Figure 2. Nucleotide alignment between the genomes ofPM2 and Cr39582 (Edward, 2004). Nucleotidesequences of both Cr39582 and PM2 were pairwisealigned with the MUSCLE alignment tool. Green barsindicate 100% nucleotide identity, brown indicates nosimilarity, and red indicates a gap at the nucleotideposition. Both the alignment and the resulting dot plothighlight the similarity of the two genomes aside from thespike protein (positions 7982-9430).

Taxonomy proposal: One (1) new species, Pseudoalteromonas virus Cr39582, in the genus Corticovirus, in the family Corticoviridae

https://helda.helsinki.fi/bitstream/10138/299804/1/2018.123B.A.v1.Corticovirus_sp.pdf

Taxonomy proposal: One (1) new species, Pseudoalteromonas virus Cr39582, in the genus Corticovirus, in the family Corticoviridae

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