violaceum to refer to strains collected from S. In particular, the Microbotryum strains from Silene latifolia analysed below are now called Microbotryum lychnidis-dioicae, but the classification is not yet settled ( Denchev et al., 2009), and so here, we will use the traditional species complex name M. The systematics of the genus is being revised to assign species names to strains with different host specificities. However, multiple sources of evidence (sequence divergence, teliospore colour, cross-mating experiments) support the view that strains on different hosts represent separate species ( Le Gac et al., 2007 De Vienne et al., 2009). violaceum, has been used for strains parasitising different host species. Until recently, the same species name, M. Microbotryum is a basidiomycete that causes anther-smut disease in many species in the plant family Caryophyllaceae. Here, we focus on the analysis of population-genetic processes dominating evolution in the non-recombining mating-type-specific regions of the smut fungus M. For example, the mating-type locus of the fungal pathogen Cryptococcus neoformans contains ∼20 genes in about 100 kb of non-recombining DNA and does not show any obvious signs of genetic degeneration ( Lengeler et al., 2002 Fraser et al., 2004). However, at present there is no solid evidence for genetic degeneration in fungal mating-type-determining regions. Indeed, it has been suggested that mating-type-determining regions of fungi, such as Cryptococcus neoformans ( Lengeler et al., 2002), Neurospora tetrasperma ( Menkis et al., 2008) and Microbotryum violaceum ( Hood, 2002 Votintseva and Filatov, 2009), represent fungal ‘sex chromosomes’. Similar processes are expected to occur in other non-recombining regions, such as plant self-incompatibility loci and fungal mating-type loci. Despite their independent evolution in different groups of animals and plants (Bull, 1983), sex chromosomes have similar properties: recombination is restricted between the X and Y chromosomes, and the male-specific non-recombining Y chromosome exhibits genetic degeneration-the loss of functional genes and accumulation of repetitive DNA. The best studied cases of such genetic degeneration include animal and plant sex chromosomes ( Charlesworth and Charlesworth, 2005). Regions that lack recombination tend to lose functional genes and accumulate junk DNA because the evolutionary fates of mutations in non-recombining regions are not independent and natural selection cannot effectively eliminate deleterious and fix advantageous mutations ( Hill and Robertson, 1966 Felsenstein, 1974). Recombination is a major determinant in genome evolution ( Gaut et al., 2007 Larracuente et al., 2008). violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining ‘sex chromosomes’ and elsewhere in the genome. We hypothesise that selfing-related reduction of recombination across the M. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. violaceum populations, which resembles that of its host species, S. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci ( π ∼0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. The analysis of DNA diversity among 19 M. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. violaceum has A1 and A2 mating types, determined by mating-type-specific ‘sex chromosomes’ that contain 1–2 Mb long non-recombining regions. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes.
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