Characterization of a Fungal Virus Representing a Novel Genus in the Family Alphaflexiviridae

Abstract

Sclerotinia sclerotiorum is an ascomycetous fungus and hosts various mycoviruses. In this study, a novel fungal alphaflexivirus with a special genomic structure, named Sclerotinia sclerotiorum alphaflexivirus 1 (SsAFV1), was cloned from a hypovirulent strain, AHS31. Strain AHS31 was also co-infected with two botourmiaviruses and two mitoviruses. The complete genome of SsAFV1 comprised 6939 bases with four open reading frames (ORFs), a conserved 5′-untranslated region (UTR), and a poly(A) tail in the 3′ terminal; the ORF1 and ORF3 encoded a replicase and a coat protein (CP), respectively, while the function of the proteins encoded by ORF2 and ORF4 was unknown. The virion of SsAFV1 was flexuous filamentous 480–510 nm in length and 9–10 nm in diameter. The results of the alignment and the phylogenetic analysis showed that SsAFV1 is related to allexivirus and botrexvirus, such as Garlic virus X of the genus Allexivirus and Botrytis virus X of the genus Botrevirus, both with 44% amino-acid (aa) identity of replicase. Thus, SsAFV1 is a novel virus and a new genus, Sclerotexvirus, is proposed to accommodate this novel alphaflexivirus.

Identification of Mycoviruses in the Pathogens of Fragrant Pear Valsa Canker from Xinjiang in China

“…For example, the growth rate of the S. sclerotiorum SZ-150 strain coinfected with Sclerotinia sclerotiorum hypovirus 1 and its related satellite RNA slowed, and the colony edge was abnormal [ 38 ]. The growth rate of the S. sclerotiorum AHS31 strain was reduced after being coinfected with botourmiaviruses and mitoviruses, and its pathogenicity decreased significantly [ 39 ]. Fungal infection with PlHV results in various phenotypes, ranging from a normal phenotype to stunted colonies with irregular colony edges [ 40 ], which is consistent with the results of the present study.…”

Molecular characterization of a novel fungal alphaflexivirus reveals potential inter-species horizontal gene transfer

“…In all plant-infecting members of the family, except for members of the genus Platypuvirus , ORF 2–4 encode the ‘triple gene block’ proteins involved in the cell-to-cell movement ( Verchot-Lubicz et al., 2010 ), and ORF5 encodes the viral capsid protein. So far, only four alphaflexiviruses that infect three plant pathogenic fungi, including Botrytis cinerea (Botrytis virus X, BVX), Botryosphaeria dothidea (Botryosphaeria dothidea botrexvirus 1, BdBV1), and Sclerotinia sclerotiorum (Sclerotinia sclerotiorum alphaflexivirus 1, SsAFV1; Sclerotinia sclerotiorum debilitation-associated RNA virus, SsDRV), have been discovered and characterized ( Howitt et al., 2006 ; Xie et al., 2006 ; Yang et al., 2021 ; Ye et al., 2023 ).…”

“…Recently, many novel mycoviruses have been characterized and identified in S. sclerotiorum ( Jia et al., 2021 ; Mu et al., 2018 ; Zhang et al., 2019 b). Eight reported mycoviruses in S. sclerotiorum belong to the order Tymovirales , three (Sclerotinia sclerotiorum deltaflexivirus 1, SsDFV1, SsDFV2, and SsDFV3) of which are positioned in the genus Deltaflexivirus within the family Deltaflexiviridea ( Hamid et al., 2018 ; Li et al., 2016 ; Mu et al., 2021 ), two (Sclerotinia sclerotiorum debilitation-associated RNA virus; SsDRV and SsDRV2) are assigned to genus Sclerodarnavirus within family Alphaflexiviridae ( Hu et al., 2014 ; Xie et al., 2006 ), two (Sclerotinia sclerotiorum mycotymovirus 1, and Sclerotinia sclerotiorum tymo-like RNA virus 4) are assigned to family Tymoviridae , and our group recently reported that SsAFV1 belongs to genus Botrexvirus within family Alphaflexiviridae ( Ye et al., 2023 ). Here, we report the characterization of a second botrexvirus, Sclerotinia sclerotiorum alphaflexivirus 2 (SsAFV2), in the hypovirulent strain 32–9 of S. sclerotiorum .…”

“…SsAFV2 contains ORF1–4 with a 5′-untranslated region (5′-UTR; 128 nt) and a 3′-UTR (151 nt). SsAFV2 has a polyadenylated structure (37 nt in length) at the 3′ terminus, like other members of the Alphaflexiviridae family ( Howitt et al., 2006 ; Yang et al., 2021 ; Ye et al., 2023 ). ORF1 putatively encodes a polyprotein (162.18 kDa) that contains three conserved domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp).…”