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. 2020 Feb 13;6(1):veaa008.
doi: 10.1093/ve/veaa008. eCollection 2020 Jan.

Molecular Fossils Reveal Ancient Associations of dsDNA Viruses With Several Phyla of Fungi

Free PMC article

Molecular Fossils Reveal Ancient Associations of dsDNA Viruses With Several Phyla of Fungi

Zhen Gong et al. Virus Evol. .
Free PMC article


Little is known about the infections of double-stranded DNA (dsDNA) viruses in fungi. Here, we use a paleovirological method to systematically identify the footprints of past dsDNA virus infections within the fungal genomes. We uncover two distinct groups of endogenous nucleocytoplasmic large DNA viruses (NCLDVs) in at least seven fungal phyla (accounting for about a third of known fungal phyla), revealing an unprecedented diversity of dsDNA viruses in fungi. Interestingly, one fungal dsDNA virus lineage infecting six fungal phyla is closely related to the giant virus Pithovirus, suggesting giant virus relatives might widely infect fungi. Co-speciation analyses indicate fungal NCLDVs mainly evolved through cross-species transmission. Taken together, our findings provide novel insights into the diversity and evolution of NCLDVs in fungi.

Keywords: endogenous viral elements; fungi; nucleocytoplasmic large DNA viruses; paleovirology; phylogenetics.


Figure 1.
Figure 1.
Phylogeny and host distribution of fungus NCLDV-like sequences. (a) Phylogenetic tree of fundsalphaviruses and fundsbetaviruses based on DNAP. Fundsalphaviruses, fundsbetaviruses, other dsDNA viruses, and P. patens ‘virus’ were labeled in green, orange, blue, and brown, respectively. This unrooted tree was reconstructed using a maximum likelihood method. Ultrafast bootstrap (UFBoot) values (>75) were shown on selected nodes. (b) Host distribution of fundsalphaviruses and fundsbetaviruses. The fungi phylogeny at the level of phylum was inferred from Tedersoo et al. (2018). The presence of fundsalphaviruses and fundsbetaviruses in fungus phylum was labeled with green solid circle and orange solid circle, respectively.
Figure 2.
Figure 2.
Evolutionary mode of fundsalphaviruses. The fundsalphavirus tree (left) is compared with its fungus host tree (right) at the level of phylum. Gray lines connect the fundsalphaviruses to their corresponding host phyla. Fungus name abbreviations: Neo_cal, Neocallimastix californiae; Pir_fin, Piromyces finnis; Ana_rob, Anaeromyces robustus; Pir_ E2, Piromyces sp. E2; Pec_rum, Pecoramyces ruminatium; Bas_mer, Basidiobolus meristosporus; Bas_het, Basidiobolus heterosporus; Cun_ele, Cunninghamella elegans; Bif_ade, Bifiguratus adelaidae; Sak_obl, Saksenaea oblongispora; Con_cor, Conidiobolus coronatus; Mor_elo, Mortierella elongate; Mor_ver, Mortierella verticillata; Zan_cul, Zancudomyces culisetae.

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