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Published in: Archives of Virology 2/2019

01-02-2019 | Brief Report

Phytophthora infestans RNA virus 2, a novel RNA virus from Phytophthora infestans, does not belong to any known virus group

Authors: Guohong Cai, Kevin Myers, William E. Fry, Bradley I. Hillman

Published in: Archives of Virology | Issue 2/2019

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Abstract

Phytophthora infestans is the causal agent of potato and tomato late blight. In this study, we obtained the complete genome sequence of a novel RNA virus from this plant pathogen, tentatively named “Phytophthora infestans RNA virus 2” (PiRV-2). The PiRV-2 genome is 11,170 nt in length and lacks a polyA tail. It contains a single large open reading frame (ORF) with short 5’ and 3’ untranslated regions. The ORF is predicted to encode a polyprotein of 3710 aa (calculated molecular weight, 410.94 kDa). This virus lacks significant similarity to any other known viruses, even in the conserved RNA-dependent RNA polymerase region. Phylogenetic analysis demonstrated that it did not cluster with any known virus group. We conclude that PiRV-2 belongs to a new virus family yet to be described. This virus was found to be faithfully transmitted through asexual reproduction.
Literature
1.
go back to reference Attoui H, Billoir F, Cantaloube JF, Biagini P, de Micco P, de Lamballerie X (2000) Strategies for the sequence determination of viral dsRNA genomes. J Virol Methods 89:147–158CrossRefPubMed Attoui H, Billoir F, Cantaloube JF, Biagini P, de Micco P, de Lamballerie X (2000) Strategies for the sequence determination of viral dsRNA genomes. J Virol Methods 89:147–158CrossRefPubMed
2.
go back to reference Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977CrossRefPubMed Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977CrossRefPubMed
3.
go back to reference Buck KW (1986) Fungal virology-an overview. In: Buck KW (ed) Fungal virology. CRC Press Inc., Boca Raton, p 1084 Buck KW (1986) Fungal virology-an overview. In: Buck KW (ed) Fungal virology. CRC Press Inc., Boca Raton, p 1084
4.
go back to reference Cai G, Myers K, Hillman BI, Fry WE (2009) A novel virus of the late blight pathogen, Phytophthora infestans, with two RNA segments and a supergroup 1 RNA-dependent RNA polymerase. Virology 392:52–61CrossRefPubMed Cai G, Myers K, Hillman BI, Fry WE (2009) A novel virus of the late blight pathogen, Phytophthora infestans, with two RNA segments and a supergroup 1 RNA-dependent RNA polymerase. Virology 392:52–61CrossRefPubMed
5.
go back to reference Cai G, Myers K, Fry WE, Hillman BI (2012) A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans. Arch Virol 157:165–169CrossRefPubMed Cai G, Myers K, Fry WE, Hillman BI (2012) A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans. Arch Virol 157:165–169CrossRefPubMed
6.
go back to reference Cai G, Hillman BI (2013) Phytophthora viruses. In: Said AG (ed) Adv virus res. Academic Press, Cambridge, pp 327–350 Cai G, Hillman BI (2013) Phytophthora viruses. In: Said AG (ed) Adv virus res. Academic Press, Cambridge, pp 327–350
7.
go back to reference Cai G, Krychiw JF, Myers K, Fry WE, Hillman BI (2013) A new virus from the plant pathogenic oomycete Phytophthora infestans with an 8 kb dsRNA genome: the sixth member of a proposed new virus genus. Virology 435:341–349CrossRefPubMed Cai G, Krychiw JF, Myers K, Fry WE, Hillman BI (2013) A new virus from the plant pathogenic oomycete Phytophthora infestans with an 8 kb dsRNA genome: the sixth member of a proposed new virus genus. Virology 435:341–349CrossRefPubMed
8.
go back to reference Cavalier-Smith T (2000) Membrane heredity and early chloroplast evolution. Trends Plant Sci 5:174–182CrossRefPubMed Cavalier-Smith T (2000) Membrane heredity and early chloroplast evolution. Trends Plant Sci 5:174–182CrossRefPubMed
9.
go back to reference Gahan PB (2005) dsRNA genetic elements, concepts and applications in agriculture, forestry and medicine. Cell Biochem Funct 23:147CrossRef Gahan PB (2005) dsRNA genetic elements, concepts and applications in agriculture, forestry and medicine. Cell Biochem Funct 23:147CrossRef
10.
go back to reference Gillings MR, Tesoriero LA, Gunn LV (1993) Detection of double-stranded RNA and virus-like particles in Australian isolates of Pythium irregulare. Plant Pathol 42:6–15CrossRef Gillings MR, Tesoriero LA, Gunn LV (1993) Detection of double-stranded RNA and virus-like particles in Australian isolates of Pythium irregulare. Plant Pathol 42:6–15CrossRef
11.
go back to reference Gulya TJ (1992) Ultrastructure of virus-like particles in Plasmopara halstedii. Can J Bot 70:334–339CrossRef Gulya TJ (1992) Ultrastructure of virus-like particles in Plasmopara halstedii. Can J Bot 70:334–339CrossRef
12.
go back to reference Hacker CV, Brasier CM, Buck KW (2005) A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene. J Gen Virol 86:1561–1570CrossRefPubMed Hacker CV, Brasier CM, Buck KW (2005) A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene. J Gen Virol 86:1561–1570CrossRefPubMed
13.
go back to reference Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109–1122CrossRefPubMed Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109–1122CrossRefPubMed
14.
go back to reference Heller-Dohmen M, Göpfert JC, Hammerschimdt R, Spring O (2008) Different pathotypes of the sunflower downy mildew pathogen Plasmopara halstedii all contain isometric virions. Mol Plant Pathol 9:777–786CrossRefPubMedPubMedCentral Heller-Dohmen M, Göpfert JC, Hammerschimdt R, Spring O (2008) Different pathotypes of the sunflower downy mildew pathogen Plasmopara halstedii all contain isometric virions. Mol Plant Pathol 9:777–786CrossRefPubMedPubMedCentral
15.
go back to reference Heller-Dohmen M, Göpfert JC, Pfannstiel J, Spring O (2011) The nucleotide sequence and genome organization of Plasmopara halstedii virus. Virol J 8:123CrossRefPubMedPubMedCentral Heller-Dohmen M, Göpfert JC, Pfannstiel J, Spring O (2011) The nucleotide sequence and genome organization of Plasmopara halstedii virus. Virol J 8:123CrossRefPubMedPubMedCentral
17.
go back to reference Honkura R, Shirako Y, Ehara Y, Yamanaka S (1983) Two types of virus-like particles isolated from downy mildew diseased rice plants. Jpn J Phytopathol 49:653–658CrossRef Honkura R, Shirako Y, Ehara Y, Yamanaka S (1983) Two types of virus-like particles isolated from downy mildew diseased rice plants. Jpn J Phytopathol 49:653–658CrossRef
18.
go back to reference Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJA (2006) The PROSITE database. Nucl Acids Res 34:D227–D230CrossRefPubMed Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJA (2006) The PROSITE database. Nucl Acids Res 34:D227–D230CrossRefPubMed
19.
go back to reference Judelson HS, Fabritius AL (2000) A linear RNA replicon from the oomycete Phytophthora infestans. Mol Gen Genet 263:395–403CrossRefPubMed Judelson HS, Fabritius AL (2000) A linear RNA replicon from the oomycete Phytophthora infestans. Mol Gen Genet 263:395–403CrossRefPubMed
20.
go back to reference Klassen GR, Kim WK, Barr DJS, Desaulniers NL (1991) Presence of double-stranded RNA in isolates of Pythium irregulare. Mycologia 83:657–661CrossRef Klassen GR, Kim WK, Barr DJS, Desaulniers NL (1991) Presence of double-stranded RNA in isolates of Pythium irregulare. Mycologia 83:657–661CrossRef
21.
go back to reference Koonin EV, Dolja VV, Morris TJ (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430CrossRefPubMed Koonin EV, Dolja VV, Morris TJ (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430CrossRefPubMed
22.
go back to reference Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292CrossRefPubMed Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292CrossRefPubMed
24.
go back to reference Kozlakidis Z, Brown NA, Jamal A, Phoon X, Coutts RHA (2009) Incidence of endornaviruses in Phytophthora taxon douglasfir and Phytophthora ramorum. Virus Genes 40:130CrossRefPubMed Kozlakidis Z, Brown NA, Jamal A, Phoon X, Coutts RHA (2009) Incidence of endornaviruses in Phytophthora taxon douglasfir and Phytophthora ramorum. Virus Genes 40:130CrossRefPubMed
25.
go back to reference Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1. J Mol Biol 305:567–580CrossRefPubMed Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1. J Mol Biol 305:567–580CrossRefPubMed
26.
go back to reference Lambden PR, Cooke SJ, Caul EO, Clarke IN (1992) Cloning of noncultivatable human rotavirus by single primer amplification. J Virol 66:1817–1822PubMedPubMedCentral Lambden PR, Cooke SJ, Caul EO, Clarke IN (1992) Cloning of noncultivatable human rotavirus by single primer amplification. J Virol 66:1817–1822PubMedPubMedCentral
27.
29.
go back to reference Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69:854–858CrossRef Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69:854–858CrossRef
30.
go back to reference Newhouse JR, Tooley PW, Smith OP, Fishel RA (1992) Characterization of double-stranded RNA in isolates of Phytophthora infestans from Mexico, the Netherlands, and Peru. Phytopathology 82:164–169CrossRef Newhouse JR, Tooley PW, Smith OP, Fishel RA (1992) Characterization of double-stranded RNA in isolates of Phytophthora infestans from Mexico, the Netherlands, and Peru. Phytopathology 82:164–169CrossRef
31.
go back to reference Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Meth 8:785–786CrossRef Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Meth 8:785–786CrossRef
32.
go back to reference Roos UP, Shaw DS (1985) Intranuclear virus-like particles in a laboratory strain of Phytophthora drechsleri. Trans Br Mycol Soc 84:340–344CrossRef Roos UP, Shaw DS (1985) Intranuclear virus-like particles in a laboratory strain of Phytophthora drechsleri. Trans Br Mycol Soc 84:340–344CrossRef
33.
go back to reference Sasai S, Tamura K, Tojo M, Herrero M-L, Hoshino T, Ohki ST, Mochizuki T (2018) A novel non-segmented double-stranded RNA virus from an Arctic isolate of Pythium polare. Virology 522:234–243CrossRefPubMed Sasai S, Tamura K, Tojo M, Herrero M-L, Hoshino T, Ohki ST, Mochizuki T (2018) A novel non-segmented double-stranded RNA virus from an Arctic isolate of Pythium polare. Virology 522:234–243CrossRefPubMed
34.
go back to reference Shirako Y, Ehara Y (1985) Composition of viruses isolated from Sclerophthora macrospora-infected rice plants. Jpn J Phytopathol 51:459–464CrossRef Shirako Y, Ehara Y (1985) Composition of viruses isolated from Sclerophthora macrospora-infected rice plants. Jpn J Phytopathol 51:459–464CrossRef
35.
go back to reference Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R (2002) Birnavirus VP1 proteins form a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif. Virology 296:241–250CrossRefPubMed Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R (2002) Birnavirus VP1 proteins form a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif. Virology 296:241–250CrossRefPubMed
36.
go back to reference Sogin ML, Silberman JD (1998) Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int J Parasitol 28:11–20CrossRefPubMed Sogin ML, Silberman JD (1998) Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int J Parasitol 28:11–20CrossRefPubMed
37.
go back to reference Styer EL, Corbett MK (1978) Intranuclear virus-like particles of Phytophthora infestans and P. parasitica var. parasitica. Mycovirus Newsl 6:16–18 Styer EL, Corbett MK (1978) Intranuclear virus-like particles of Phytophthora infestans and P. parasitica var. parasitica. Mycovirus Newsl 6:16–18
38.
go back to reference Suzuki N, Sugawara M, Kusano T, Mori H, Matsuura Y (1994) Immunodetection of rice dwarf phytoreoviral proteins in both insect and plant hosts. Virology 202:41–48CrossRefPubMed Suzuki N, Sugawara M, Kusano T, Mori H, Matsuura Y (1994) Immunodetection of rice dwarf phytoreoviral proteins in both insect and plant hosts. Virology 202:41–48CrossRefPubMed
39.
40.
go back to reference Tooley PW, Hewings AD, Falkenstein KF (1989) Detection of double-stranded RNA in Phytophthora infestans. Phytopathology 79:470–474CrossRef Tooley PW, Hewings AD, Falkenstein KF (1989) Detection of double-stranded RNA in Phytophthora infestans. Phytopathology 79:470–474CrossRef
41.
go back to reference Yokoi T, Takemoto Y, Suzuki M, Yamashita S, Hibi T (1999) The nucleotide sequence and genome organization of Sclerophthora macrospora virus B. Virology 264:344–349CrossRefPubMed Yokoi T, Takemoto Y, Suzuki M, Yamashita S, Hibi T (1999) The nucleotide sequence and genome organization of Sclerophthora macrospora virus B. Virology 264:344–349CrossRefPubMed
42.
go back to reference Yokoi T, Yamashita S, Hibi T (2003) The nucleotide sequence and genome organization of Sclerophthora macrospora virus A. Virology 311:394–399CrossRefPubMed Yokoi T, Yamashita S, Hibi T (2003) The nucleotide sequence and genome organization of Sclerophthora macrospora virus A. Virology 311:394–399CrossRefPubMed
Metadata
Title
Phytophthora infestans RNA virus 2, a novel RNA virus from Phytophthora infestans, does not belong to any known virus group
Authors
Guohong Cai
Kevin Myers
William E. Fry
Bradley I. Hillman
Publication date
01-02-2019
Publisher
Springer Vienna
Published in
Archives of Virology / Issue 2/2019
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI
https://doi.org/10.1007/s00705-018-4050-0

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