Repeat induced point mutation (RIP), a mechanism\ud causing hypermutation of repetitive DNA sequences\ud in fungi, has been described as a ‘genome defense’ which\ud functions to inactivate mobile elements and inhibit their\ud deleterious effects on genome stability. Here we address\ud the interactions between RIP and transposable elements in\ud the Microbotryum violaceum species complex. Ten strains\ud of M. violaceum, most of which belong to different species\ud of the fungus, were all found to contain intragenomic\ud populations of copia-like retrotransposons. Intragenomic\ud DNA sequence variation among the copia-like elements\ud was analyzed for evidence of RIP. Among species with\ud RIP, there was no significant correlation between the frequency\ud of RIP-induced mutations and inferred transposition\ud rate based on diversity. Two strains of M. violaceum,\ud from two different plant species but belonging to the same\ud fungal lineage, contained copia-like elements with very\ud low diversity, as would result from a high transposition\ud rate, and these were also unique in showing no evidence of\ud the hypermutation patterns indicative of the RIP genome\ud defense. In this species, evidence of RIP was also absent\ud from a Class II helitron-like transposable element. However,\ud unexpectedly the absolute repetitive element load was\ud lower than in other strains
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