Complete genome sequence of a novel alternavirus infecting the fungus Ilyonectria crassa

Abstract

A novel dsRNA mycovirus named Ilyonectria crassa alternavirus 1 (IcAV1) was found in Ilyonectria crassa isolate NW-FVA 1829. The fungus was isolated from an ash (Fraxinus excelsior L.) necrotic trunk disc infected with Hymenoscyphus fraxineus [(T. Kowalski) Baral, Queloz, Hosoya] causing ash dieback. The complete genome of IcAV1 is composed of three segments, each containing a single ORF on the positive-sense RNA. The extreme 5’ UTRs of dsRNA 1 (3604 bp), dsRNA 2 (2547 bp), and dsRNA 3 (2518 bp) share a conserved hexadecamer sequence (5’-GGCTGTGTGTTTAGTT-3’) and are capped. The 3’ UTRs are polyadenylated. In silico analysis showed that the viral RdRP is encoded on dsRNA 1 and the capsid-protein subunits are encoded on dsRNA 3. Maximum-likelihood analysis of the aa sequence of the viral RdRP showed that IcAV1 clusters with alternaviruses from Fusarium spp., while the type member of the proposed family "Alternaviridae", Alternaria alternata virus 1 (AaV1), formed a clade together with Stemphylium lycopersici mycovirus (SlV). The function of the protein encoded on segment 2 is unknown. Based on its genome organization and its phylogenetic position, IcAV1 is suggested to be a new member of the proposed family "Alternaviridae". This is the first report of a mycovirus infecting I. crassa.

A Novel Strain of Fusarium oxysporum Alternavirus 1 Isolated from Fusarium oxysporum f. sp. melonis Strain T-BJ17 Confers Hypovirulence and Increases the Sensitivity of Its Host Fungus to Difenoconazole and Pydiflumetofen

“…It was stated that the criteria for demarcating species should consider the number of dsRNA segments and the presence and homology of dsRNA 4 (https://ictv.global/files/ proposals/approved?fid=11959#block-teamplus-page-title, accessed on 5 March 2024). Thus far, eighteen mycoviruses have been assigned as members of the family Alternaviridae [11,[13][14][15][16][17][18][19][47][48][49][50][51][52][53][54][55]. Except for FaAV1, which is composed of two dsRNA segments [13], the remaining seventeen alternaviruses contain three or four dsRNA segments [11,[14][15][16][17][18][19][47][48][49][50][51][52][53][54][55].…”

“…It was stated that the criteria for demarcating species should consider the number of dsRNA segments and the presence and homology of dsRNA 4 ( , accessed on 5 March 2024). Thus far, eighteen mycoviruses have been assigned as members of the family Alternaviridae [ 11 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. Except for FaAV1, which is composed of two dsRNA segments [ 13 ], the remaining seventeen alternaviruses contain three or four dsRNA segments [ 11 , 14 , 15 , 16 , 17 , 18 , 19 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ].…”

“…Thus far, eighteen mycoviruses have been assigned as members of the family Alternaviridae [ 11 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. Except for FaAV1, which is composed of two dsRNA segments [ 13 ], the remaining seventeen alternaviruses contain three or four dsRNA segments [ 11 , 14 , 15 , 16 , 17 , 18 , 19 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. Among them, eleven alternaviruses, namely Aspergillus heteromorphus alternavirus 1 (AheAV1) [ 49 ], Cordyceps chanhua alternavirus 1 (CcAV1) [ 52 ], Dactylonectria torresensis alternavirus 1 (DtAV1) [ 53 ], FgAV1 [ 14 ], FiAV1 [ 15 ], FnAV1 [ 16 ], FpgAV1 [ 18 ], FpAV1 [ 17 ], Ilyonectria crassa alternavirus 1 (IcAV1) [ 51 ], Ilyonectria robusta alternavirus 1 (IrAV1) [ 53 ], and Suillus luteus alternavirus 1 (SluAV1) [ 55 ], contain three dsRNA segments, while six alternaviruses, including AaV1 [ 47 ], Aspergillus foetidus virus (AfV) [ 54 ], Aspergillus virus 341 (AsV341) [ …”

“…Except for FaAV1, which is composed of two dsRNA segments [ 13 ], the remaining seventeen alternaviruses contain three or four dsRNA segments [ 11 , 14 , 15 , 16 , 17 , 18 , 19 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. Among them, eleven alternaviruses, namely Aspergillus heteromorphus alternavirus 1 (AheAV1) [ 49 ], Cordyceps chanhua alternavirus 1 (CcAV1) [ 52 ], Dactylonectria torresensis alternavirus 1 (DtAV1) [ 53 ], FgAV1 [ 14 ], FiAV1 [ 15 ], FnAV1 [ 16 ], FpgAV1 [ 18 ], FpAV1 [ 17 ], Ilyonectria crassa alternavirus 1 (IcAV1) [ 51 ], Ilyonectria robusta alternavirus 1 (IrAV1) [ 53 ], and Suillus luteus alternavirus 1 (SluAV1) [ 55 ], contain three dsRNA segments, while six alternaviruses, including AaV1 [ 47 ], Aspergillus foetidus virus (AfV) [ 54 ], Aspergillus virus 341 (AsV341) [ 50 ], FoAV1 [ 11 ], FsAV1 [ 19 ], and Stemphylium lycopersici alternavirus 1 (SlAV1) [ 48 ], contain four dsRNA segments. Usually, dsRNA 1 encodes RdRp, dsRNA 2 encodes a conserved protein with an unknown function, dsRNA 3 encodes capsid protein (CP), and dsRNA 4, when present, encodes a non-conserved protein with an unknown function that is often non-homologous among alternaviruses.…”