Clonality despite sex: the evolution of host-associated sexual neighborhoods in the pathogenic fungus Penicillium marneffei

Abstract

Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of P. marneffei. Genome wide comparisons reveal that all the genes required for meiosis are present in P. marneffei, mating type genes are arranged in a similar manner to that found in other heterothallic fungi, and there is evidence of a putatively meiosis-specific mutational process. Experiments suggest that recombination between isolates of compatible mating types may occur during mammal infection. Population genetic data from 34 isolates from bamboo rats in India, Thailand and Vietnam, and 273 isolates from humans in China, India, Thailand, and Vietnam show that recombination is most likely to occur across spatially and genetically limited distances in natural populations resulting in highly clonal population structure yet sexually reproducing populations. Predicted distributions of three different spatial genetic clusters within P. marneffei overlap with three different bamboo rat host distributions suggesting that recombination within hosts may act to maintain population barriers within P. marneffei.

Figure 1. Mating type idiomorph of P. marneffei.

A) A dot plot showing similarity between strains FRR2161 and FRR3482 similarity across the 7 kb covering MAT loci. B) Gene cartoon showing arrangement of genes in the MAT idiomorphs. Grey regions are areas of high homology, and black lines are small segments of rearrangement. Coding regions of MAT alpha and HMG genes are shown in black, flanking genes with high homology are shown in grey, and hypothetical genes with low homology are shown in white. Arrows indicate the direction of transcription.

Figure 2. Biased mutation in P. marneffei.

Nucleotide bias in P. marneffei. A) AG dinucleotide frequency across the entire genome of P. marneffei shows a non-normal distribution consistent with patterns of RIP-like process B) Comparison between the types of mutations from the inferred ancestral state shows a bias in transitions and towards G to A and C to T mutations in particular.

Figure 3. Correspondence between genetic diversity and spatial location.

A) Unrooted neighborjoining tree of genetic distances between isolates labelled with the colour each isolation locality. B) Genetic clusters inferred using DAPC and isolates coloured according to cluster. C) Spatial distribution of DAPC clusters.

Figure 4. EBURST diagram showing clones with mating types.

Mating types are shown for each clone composed of more than a single isolate. MAT1-1-1 isolates are labelled with a red 1, and MAT1-2-1 isolates are labelled with a blue 2. The four genotypes that have both mating types are labelled by Microsatellite Type (MT) number.

Figure 5. Predicted distributions of P. marneffei genetic clusters and bamboo rat species.

A) Niche model distribution of Cluster 1. B) Niche model distribution of Cluster 2. C) Niche model distribution of Cluster 3. D) IUCN distribution of Cannomys badius. E) IUCN distribution of Rhizomys sinensis. F) IUCN distribution of Rhizomys sumatrensis. G) Niche model distribution of C. badius. H) Niche modeldistribution of R. sinensis. I) Predicted distribution of R. sumatrensis.