Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum

Abstract

Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the family Totiviridae, one alphaendornavirus in the family Endornaviridae, two mitoviruses in the family Mitoviridae, and one narnavirus belonging to the family Narnaviridae. The presence of the co-infecting viruses was confirmed by sequencing the RT-PCR products generated from total nucleic acids extracted from COLB. This study shows that the mycovirome of a single N. parvum strain is highly diverse and distinct from that previously described in N. parvum strains isolated from grapevines.

Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

“…Sclerotinia sclerotiorum endornavirus 3/SX276 (QOE77938.1), which was isolated from S. sclerotiorum strain in China, is a betaendornavirus, while Sclerotinia sclerotiorum endornavirus 3 (AWY10956.1), which was associated with S. sclerotiorum strain in Australia, is a member of Alphaendornavirus. RdRp aa sequences of Sclerotinia sclerotiorum endornavirus 3 (AWY10956.1) shares 59% (310/529) aa identity and 73% similarity (389/529) to that of Neofusicoccum parvum endornavirus 1 [ 45 ], which is located on the Cluster Ib ( Figure 4 ). Sclerotinia sclerotiorum endornavirus 4, −5, −6, −7, 8, −9, −10 have been reported with incomplete genome sequence.…”

Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan

“…The ascomycetous family Botryosphaeriaceae includes many important phyotpathogenic fungi such as members of the genera Botryosphaeria , Neofusicoccum , and Diploidia. Whereas some members of the first two genera have been explored as viral hosts ( Wang et al., 2014 ; Marais et al., 2021 ), the third one has not. Diplodia seriata (anamorph of Botryosphaeria obtusa ) is a phytopathogenic ascomycete that causes fruits rot, leaf spot, canker, leaf chlorosis and trunk dieback in many woody and herbaceous plants ( Phillips et al., 2007 ; Farr and Rossman, 2022 ).…”

Grapevine virome and production of healthy plants by somatic embryogenesis

“…Therefore, the epiphytic fungal community and the mycoviruses associated with it had been influenced by these antifungal treatments. Seven of the putative mycoviruses detected (Table S1) had a very high sequence homology with mycoviruses that were previously identified, such as Sclerotinia sclerotiorum virga‐like virus 1 (Jia et al ., 2021 ), or mycoviruses identified in grapevine, such as Gremmeniella abietina RNA virus MS1, Plasmopara viticola lesion‐associated vivivirus 1 and Erysiphe necator‐associated narnavirus 33 associated with grapevine downy and powdery mildew lesions (Chiapello et al ., 2020a ) and Neofusicoccum parvum mitovirus 3 associated with grapevine trunk disease (Marais et al ., 2021 ). In the metatranscriptome, we also found three RNA segments corresponding to grapevine‐associated jivivirus 1 (GaJV1), which was originally identified in Plasmopara viticola ‐infected grapevine samples and that is considered a plant virus (Chiapello et al ., 2020b ).…”

“…The positive or negative effects that these virus‐infected endophytic or epiphytic fungi can induce in host plants make mycoviruses a class of viruses to be carefully considered for gaining a comprehensive understanding of plant–environment interactions. Mycoviruses associated with culturable fungal pathogens, such as Botrytis cinerea (Ruiz‐Padilla et al ., 2021 ), Neofusicoccum parvum (Marais et al ., 2021 ), grapevine trunk pathogens (Nerva et al ., 2019a ) or non‐culturable endophytes/epiphytes (Chiapello et al ., 2020a ) have also been identified in grapevine by HTS. In the case of mixed samples, containing RNAs from plants and its associated fungi, the distinction among plant and fungal viruses can be difficult (Chiapello et al ., 2020b ; Silva et al ., 2021 ).…”