Evolutionary origin of 2A-like sequences in Totiviridae genomes

Lima, Juliana Gabriela Silva de; Teixeira, Diego Gomes; Freitas, T. T.; Lima, J. A. S.; Lanza, Daniel Carlos Ferreira

doi:10.1016/j.virusres.2018.10.011

Cited by 27 publications

(19 citation statements)

References 61 publications

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“…As more and more virus-like sequences have been identified in recent years, classification of the family Totiviridae may need to be revised [39–42]. Discovery of new dsRNA viruses with ancient origins may provide insight for understanding the evolution and distribution of RNA viruses [43].…”

Section: Discussionmentioning

confidence: 99%

Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence

Liu

Sniezko³

et al. 2019

Virol J

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Background Mycoviruses were recently discovered in the white pine blister rust (WPBR) fungus Cronartium ribicola (J.C. Fisch.). Detection and characterization of their double stranded RNA (dsRNA) would facilitate understanding of pathogen virulence and disease pathogenesis in WPBR systems. Methods Full-length cDNAs were cloned from the dsRNAs purified from viral-infected C. ribicola, and their cDNA sequences were determined by DNA sequencing. Evolutionary relationships of the dsRNAs with related mycoviruses were determined by phylogenetic analysis. Dynamic distributions of the viral RNAs within samples of their fungal host C. ribicola were investigated by measurement of viral genome prevalence and viral gene expression. Results In this study we identified and characterized five novel dsRNAs from C. ribicola, designated as Cronartium ribicola totivirus 1–5 (CrTV1 to CrTV5). These dsRNA sequences encode capsid protein and RNA-dependent RNA polymerase with significant homologies to dsRNA viruses of the family Totiviridae. Phylogenetic analysis showed that the CrTVs were grouped into two distinct clades. CrTV2 through CrTV5 clustered within the genus Totivirus. CrTV1 along with a few un-assigned dsRNAs constituted a distinct phyletic clade that is genetically distant from presently known genera in the Totiviridae family, indicating that CrTV1 represents a novel genus in the Totiviridae family. The CrTVs were prevalent in fungal samples obtained from infected western white pine, whitebark pine, and limber pines. Viral RNAs were generally expressed at higher levels during in planta mycelium growth than in aeciospores and urediniospores. CrTV4 was significantly associated with C. ribicola virulent pathotype and specific C. ribicola host tree species, suggesting dsRNAs as potential tools for dissection of pathogenic mechanisms of C. ribicola and diagnosis of C. ribicola pathotypes. Conclusion Phylogenetic and expression analyses of viruses in the WPBR pathogen, C. ribicola, have enchanced our understanding of virus diversity in the family Totiviridae, and provided a potential strategy to utilize pathotype-associated mycoviruses to control fungal forest diseases.

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Section: Discussionmentioning

confidence: 99%

Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence

Liu

Sniezko³

et al. 2019

Virol J

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“…ORF2 (779 aa; nt positions 3,207-5,543) codes for a putative RNAdependent RNA polymerase (RdRp) and shares the highest BLASTx identity (58.64%; query coverage, 99%) with PsRV1 RdRp (LC467965). No H-type RNA pseudoknot, which could stimulate frameshifting, was detected next to the slippery sequence, although a pseudoknot was predicted at a 37-nt distance from the ORF1 stop codon using HPknotter [4] (Fig. 1B).…”

Section: Sequence Propertiesmentioning

confidence: 99%

“…Viruses resembling Giardia lamblia virus (GLV), the sole classified member of the genus Giardiavirus, family Totiviridae (ICTV Master Species List 2018b.v2 at https ://talk.ictvo nline .org/), have recently been detected in arthropods, fish and fungi [4,10,14]. Phylogenetic analysis based on RdRp sequences (Fig.…”

Section: Sequence Propertiesmentioning

confidence: 99%

Complete genome sequence of a novel toti-like virus from the plant-pathogenic oomycete Phytophthora cactorum

Poimala

Vainio

2020

Arch Virol

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This report describes the complete genome sequence of a double-stranded RNA (dsRNA) virus infecting the oomycetous plant pathogen Phytophthora cactorum. The virus genome consists of a single dsRNA segment of 5699 bp with two open reading frames predicted to overlap with each other and encoding a putative capsid protein of 705 aa and an RNA-dependent RNA polymerase of 779 aa. Sequence comparisons indicated that this virus, designated as “Phytophthora cactorum RNA virus 1” (PcRV1), shares the highest sequence similarity with the unclassified Pythium splendens RNA virus 1 (58% RdRp aa sequence identity). Phylogenetic analysis revealed that these two oomycete viruses group together with Giardia lamblia virus (GVL; family Totiviridae) and several unclassified toti-like viruses from arthropods, fish and fungi. This is the first report of a toti-like virus in a member of the genus Phytophthora and the first virus characterized in P. cactorum.

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“…Totiviruses have been discovered in excavata, alveolate, fungi, arthropods, fish, and oomycetes [24,48,56]. The family Totiviridae contains five genera: Totivirus, Giardiavirus, Victorivirus, Leishmaniavirus, and Trichomonasvirus (ICTV, Virus Taxonomy: 2020 Release) and there are many unclassified toti-like viruses.…”

Section: Pythium Ultimum Rna Virusmentioning

confidence: 99%

Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic Oomycete Globisporangium ultimum

Fukunishi

Sasai

Tojo

et al. 2021

Viruses

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To further classify the oomycete viruses that have been discovered in recent years, we investigated virus infection in the plant-parasitic oomycete Globisporangium ultimum in Japan. Double-stranded RNA detection, high-throughput sequencing, and RT-PCR revealed that the G. ultimum isolate UOP226 contained two viruses related to fusarivirus and totivirus, named Pythium ultimum RNA virus 1 (PuRV1) and Pythium ultimum RNA virus 2 (PuRV2), respectively. Phylogenetic analysis of the deduced amino acid sequence of the RNA-dependent RNA polymerase (RdRp) showed that fusari-like PuRV1 belonged to a different phylogenetic group than Plasmopara viticola lesion-associated fusari virus (PvlaFV) 1–3 from oomycete Plasmopara viticola. Codon usage bias of the PuRV1 RdRp gene was more similar to those of fungi than Globisporangium and Phytophthora, suggesting that the PuRV1 ancestor horizontally transmitted to G. ultimum ancestor from fungi. Phylogenetic analysis of the deduced amino acid sequence of the RdRp of toti-like PuRV2 showed a monophyletic group with the other toti-like oomycete viruses from Globisporangium, Phytophthora, and Pl. viticola. However, the nucleotide sequences of toti-like oomycete viruses were not so homologous, suggesting the possibility of convergent evolution of toti-like oomycete viruses.

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Evolutionary origin of 2A-like sequences in Totiviridae genomes

Cited by 27 publications

References 61 publications

Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence

Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence

Complete genome sequence of a novel toti-like virus from the plant-pathogenic oomycete Phytophthora cactorum

Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic Oomycete Globisporangium ultimum

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