The impact of genome defense on mobile elements in Microbotryum

Abstract

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

Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi

“…In Drosophila miranda , TEs played an early and important role in the degeneration of the neo-Y chromosome (Bachtrog, 2005). We detected RIP-like footprints in Microbotryum genomes, but this genome defense mechanism was not sufficient to control TE proliferation without recombination, as previously noted in some Microbotryum species (Johnson et al ., 2010; Horns et al ., 2017).…”

“…In the Microbotryum species parasitizing Dianthus carthusianorum , a burst of Ty3 retroelements has caused a massive accumulation of this element in a short period of time, in spite of RIP-like activity (Horns et al ., 2017). In Microbotryum genomes, a RIP-like activity targets TCG trinucleotides (CGA on the reverse complement strand) rather than di-nucleotides as in ascomycetes (Hood et al ., 2005; Johnson et al ., 2010; Horns et al ., 2012).…”

Transposon-associated epigenetic silencing duringPleurotus ostreatuslife cycle

“… 18 , 19 In ascomycetes, transposons can be inactivated by DNA methylation linked to RIP mutations, 20 whereas in basidiomycetes this mechanism has been examined in silico in members of the Pucciniomycotina 21 and in the ustilaginomycete Microbotrium violaceum . 22 A related mechanism called methylation-induced premeiotically, has been detected in Ascobolus immersus and in the basidiomycete Coprinus cinereus and it displays similar hallmarks with RIP. 23 , 24 Distinct DNA methylation patterns have been observed in some fungal lineages while in others this mechanism seems to be absent.…”

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

“…However, Dnmt1 MTases involved in RIP bias may have evolved to recognize dinucleotides other than CpG. In the basidiomycete Microbotryum violaceum , C to T mutation bias in TEs occurs preferentially at a trinucleotide TpCpG site [ 29 ], suggesting the involvement of a Dnmt1 MTase specific to the CpG di-nucleotide. This mutation bias at CpG di-nucleotide is consistent with the model of mutation via methylation-mediated deamination of 5-methyl cytosine (5mC) previously describe in human genetic disease [ 30 ].…”