Clonal reproduction in fungi

Abstract

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305-E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.

The frequency of sex in fungi

“…With the onset of next generation sequencing to measure these rates, such approaches are likely to be readily adopted. Taylor et al [111] proposed that LD decay, the decrease in LD between pairs of sites increasing distances apart in the genome, could be a useful means of addressing the relative importance of recombination in a fungal life cycle across the diversity of species, and this seems like a useful approximation. Although LD can be influenced by a number of factors, such as intrinsic differences in recombination rates, background selection and demographic history, focusing on genome-wide estimates and categories of nearly neutral mutations could avoid region-specific problems with selection and recombination rate variation.…”

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…Flores-L opez and Machado (2011) b Ni et al (2013) b,c Feil (2010) b Gatei et al (2007) b,e Taylor (2015) b,c Fraser et al (2007) b Gelanew et al (2010) d Xu (2006) b,e…”

“…According to Taylor (2015), in fungi, clonality, which the author equates to restrained recombination, can have extrinsic and intrinsic cause. Extrensic causes include dispersal (bottleneck/founder effects leading to a deficiency of mating types and adaptation to new hosts) and hybridization between very divergent parental genotypes, leading to the impossibility of meiosis, a mechanism invoked also by Avise (2015) to explain asexuality in clonal vertebrates.…”

“…In fungi, it has been proposed that, although the sexual machinery was present in fungi, they 'retain sex' and their populations are often clonal (Heitman, 2006). Taylor (2015) defends the view that intrinsic obstacles to recombination exist in fungi.…”

In the light of evolution IX: Clonal reproduction: Alternatives to sex

“…Within this span of time, the clonality status of E. coli has evolved as different and more discriminant sequencing methods have been used. John Taylor et al (19) review current knowledge on recombination and clonality in fungi and yeasts. These organisms include several important pathogens, such as Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans.…”