A 1.5 Mb continuous endogenous viral region in the arbuscular mycorrhizal fungusRhizophagus irregularis

Abstract

Most fungal viruses are RNA viruses and no double-stranded DNA virus that infects fungi is known to date. A recent study identified DNA polymerase genes that originated from large dsDNA viruses in genomes of basal fungi, suggesting the existence of dsDNA viruses infecting fungi. In this study, we searched for viral infection signatures in chromosome-level assemblies of an arbuscular mycorrhizal fungus,Rhizophagus irregularis. We identified a continuous 1.5 Mb putative viral region on a chromosome ofR. irregularisstrain 4401. Phylogenetic analysis revealed that the viral region is related to members of familyAsfarviridaein phylumNucelocytoviricota. Single-copy marker genes of theNucelocytoviricotawere detected as single copies in the viral region. Furthermore, this viral region was not found in other four strains ofR. irregularisand showed less invasive signals of fungal transposable elements than other genomic regions. These results suggest a recent and single insertion of a large dsDNA viral genome in this fungal strain, providing strong evidence for the recent infection of a dsDNA virus to the fungus.

Eukaryotic genomic data uncover an extensive host range of mirusviruses

“…10 In general, the viral sequences within eukaryotic genome assemblies can be categorized into three types: transferred genes, integrated viral genome fragments, and free viral genomes. [12][13][14] The previously reported endogenized mirusviral sequences and the circular genome correspond to the latter two types, respectively. These three types of evidence strongly suggest that eukaryotes containing viral signals have acted as the hosts of viruses.…”

Pathogenicity, genomic analysis and structure of abalone asfa-like virus: evidence for classification in the family Asfarviridae

“…In the E. marginata genomic analysis, a considerable number of coding sequences homologous to ASFV and AbALV genes were found in one scaffold (accession no. BMAT01005152.1) that formed independently of the host genome scaffolds [13,14]. It is likely that an unknown virus closely related to AbALV and ASFV had infected or was present in the E. marginata used for the genome analysis.…”

“…The sequence of the type B DNA polymerase (PolB) gene of the Heterocapsa circularisquama DNA virus, which infects marine dinoflagellates, is highly similar to the PolB gene sequence of ASFV [11]. Additionally, published genomic data of the gastropod Elysia marginata [12] include a scaffold containing multiple coding sequences homologous to the gene of the ASFV genome [13,14]. Furthermore, metagenomic analyses have identified sequences homologous to the ASFV in marine [15,16] and freshwater [17] sources.…”

“…The partial genome sequence was conserved in synteny with the genome of ASFV, and we proposed abalone asfa-like virus (AbALV) as a tentative name for the causative virus [19]. Phylogenetic analysis of its core gene sets indicated that AbALV is most closely related to ASFV among currently known viruses [13,14,16,19]. Here, we discuss the rationale for including AbALV in the family Asfarviridae based on analyses of the host and AbALV whole genome sequence as well as electron microscopic observations of the virus.…”

“…Furthermore, metagenomic analyses have identified sequences homologous to the ASFV in marine [15,16] and freshwater [17] sources. ASFV-like integrated elements have also been found in the genomes of ticks [18] and fungi [14], suggesting that the ancestors of these organisms were infected with ASFV-like viruses. ASFV and related viruses appear to be more diverse than previously thought.…”