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

Abstract

Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.

Uncovering a Complex Virome Associated with the Cacao Pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata

“…Here, two major ORF-associated domains were found: Tymovirus , RdRp, and (+) RNA virus helicase core dom, which have been identified in several virus types [ 113 ] including a variety of plant virus families [ 114 ]. In addition, Luo and collaborators (2022) [ 115 ], analyzing S. sclerotiorum , identified a new endornavirus called Scelrotinia sclerotiorum endornavirus 11 (SsEV11), suggesting that there is remarkable phylogenetic diversity in the Endornaviridae family and corroborating previous findings that viruses of this family can be found in fungi. In this respect, Cao and collaborators (2022) [ 116 ] studied Ceratobasidium infected with three endornaviruses with significantly upregulated micro-RNA-like RNAs (Cer-milRNAs) and identified transcription factors, suggesting an effect of viral infection on the control of regulatory networks and growth and development of the fungus.…”

Seven new mycoviruses identified from isolated ascomycetous macrofungi

“…Endornaviridae includes unique, persistent viruses with symbiotic properties that are capable of infecting diverse eukaryotes, such as plants, fungi, and protists ( Fukuhara, 2019 ). The genus Alphaendornavirus is capable of infecting basidiomycetes, oomycetes, and plants, with a diverse host range and genome characteristics ( Ong et al., 2016 ; Luo et al., 2022 ). Alphaendornavirus includes three major subclusters (1a, 1b, 1c in Fig.…”

Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines (Vitis vinifera L.) in Idaho, USA

“…Incidentally, the name Gammaendornavirus was proposed for a phylogroup within the genus Alphaendornavirus earlier [ 42 ], but the proposal was based on an RdRP phylogeny only and for a relatively small number of endornavirus sequences available at the time; this proposal was later rejected [ 5 ]. It was put forward again recently [ 43 ] for an alleged lineage of endorna-like viruses based on RdRP phylogeny only; however, it was, in fact, applied to a lineage of virga- and negev-like viruses, which did not include PvEV-3 and GcEV-1, and actually included no endorna- or endorna-like viruses [ 43 ], apparently in error. Here, we propose the use of this name to designate a new lineage of endornaviruses, constituting a sister clade to alphaendornaviruses in the phylogenies of the RdRP and HEL domains and having a similar domain architecture in their polyproteins.…”