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

Xin Luo,Jiatao Xie,Jichun Jia,Jiasen Cheng,Bo Li,Yang Lin,Jie Duan,Tao Chen,Daohong Jiang,Xiao Yu,Yanping Fu

doi:10.3390/v14030456

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.

Highlights

Endornaviruses are a group of virionless viruses with linear, (+) ssRNA genome
Complete nucleotide sequence of Scelrotinia sclerotiorum endornavirus 11 (SsEV11) had no significant identity to other viruses, even at the most similar parts
Nucleotide identity between SsEV11 and other viruses were less than 75% (Table 1), suggesting that SsEV11 represents a novel species in the genus Betaendornavirus

Summary

Introduction

Endornaviruses are a group of virionless viruses with linear, (+) ssRNA genome. The genome size of endornaviruses is various, with a range of 9.7–17.6 kb [1,2]. With very rare exceptions [3], endornaviruses typically have a large open reading flame (ORF) that encodes a polyprotein with methyltransferase (MTR), helicase (Hel), glycosyltransferase (GTR), and RNA-dependent RNA polymerase (RdRp) [2]. Endornaviruses are phylogenetically related to alpha viruses, and have been grouped in the Family Endornaviridae; currently, two genera, namely Alphaendornavirus and Betaendornavirus, have been established in this family based on their genome size, host, and the presence of unique domains [4–6]. Viruses that belong to Alphaendornavirus were identified from plants, fungi, and oomycetes [7–13], while viruses in genus Betaendornavirus infect fungi only [2]. Endorna-like viruses were found in animals, such as nematodes, mites, and insects [14–17], but their taxonomic status has not been determined

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Conclusion