Vegetative incompatibility (vic), a form of nonself allorecognition, operates widely in filamentous fungi and restricts transmission of virulence-attenuating hypoviruses in the chestnut blight fungus Cryphonectria parasitica. We report here the use of a polymorphism-based comparative genomics approach to complete the molecular identification of the genetically defined C. parasitica vic loci with the identification of vic1 and vic3. The vic1 locus in the C. parasitica reference strain EP155 consists of a polymorphic HET-domain-containing 771-aa ORF designated vic1a-2, which shares 91% identity with the corresponding vic1a-1 allele, and a small (172 aa) idiomorphic DUF1909-domain-containing ORF designated vic1b-2 that is absent at the vic1-1 locus. Gene disruption of either vic1a-2 or vic1b-2 in strain EP155 eliminated restrictions on virus transmission when paired with a vic1 heteroallelic strain; however, only disruption of vic1a-2 abolished the incompatible programmed cell death (PCD) reaction. The vic3 locus of strain EP155 contains two polymorphic ORFs of 599 aa (vic3a-1) and 102 aa (vic3b-1) that shared 46 and 85% aa identity with the corresponding vic3a-2 and vic3b-2 alleles, respectively. Disruption of either vic3a-1 or vic3b-1 resulted in increased virus transmission. However, elimination of PCD required disruption of both vic3a and vic3b. Additional allelic heterogeneity included a sequence inversion and a 8.5-kb insertion containing a LTR retrotransposon sequence and an adjacent HET-domain gene at the vic1 locus and a 7.7-kb sequence deletion associated with a nonfunctional, pseudo vic locus. Combined gene disruption studies formally confirmed restriction of mycovirus transmission by five C. parasitica vic loci and suggested dedicated roles in allorecognition. The relevance of these results to the acquisition and maintenance of vic genes and the potential for manipulation of vic alleles for enhanced mycovirus transmission are discussed.A LLORECOGNITION genetic systems, which provide the ability to distinguish self from nonself, play important functional roles in microbial and multicellular organisms. These systems range from restriction endonucleases in bacteria (Meselson and Yuan 1968) to somatic histocompatibility in protocordates (De Tomaso et al. 2005), self-infertility in plants (Nasrallah 2005), and innate immunity in vertebrates (Medzhitov and Janeway 2002) (reviewed by Aanen et al. 2008;Nydam and De Tomaso 2011;Rosengarten and Nicotra 2011). Allorecognition operates widely in filamentous fungi in both the sexual and the vegetative growth phases (Saupe 2000). The role of the mating-type locus in controlling sexual recognition and promoting outbreeding in yeast and filamentous fungi is well understood (reviewed by Coppin et al. 1997). It is also known that somatic or vegetative fusion of fungal cells (termed "anastomosis") occurs at a high frequency within and between individuals promoting network formation (Rayner 1996) and facilitating foraging, the pooling of resources (Rayner 1996), ...