Global Analyses of Multi-Locus Sequence Typing Data Reveal Geographic Differentiation, Hybridization, and Recombination in the Cryptococcus gattii Species Complex

Abstract

Cryptococcus gattii species complex (CGSC) is a basidiomycete haploid yeast and globally distributed mammalian pathogen. CGSC is comprised of six distinct lineages (VGI, VGII, VGIII, VGIV, VGV, and VGVI); however, the geographical distribution and population structure of these lineages is incompletely described. In this study, we analyze published multi-locus sequence data at seven loci for 566 previously recorded sequence types (STs) encompassing four distinct lineages (VGI, VGII, VGIII, and VGIV) within the CGSC. We investigate indicators of both clonal dispersal and recombination. Population genetic analyses of the 375 STs representing 1202 isolates with geographic information and 188 STs representing 788 isolates with ecological source data suggested historically differentiated geographic populations with infrequent long-distance gene flow. Phylogenetic analyses of sequences at the individual locus and of the concatenated sequences at all seven loci among all 566 STs revealed distinct clusters largely congruent with four major distinct lineages. However, 23 of the 566 STs (4%) each contained alleles at the seven loci belonging to two or more lineages, consistent with their hybrid origins among lineages. Within each of the four major lineages, phylogenetic incompatibility analyses revealed evidence for recombination. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across all samples. Together, our results suggest evidence for historical geographical differentiation, sexual recombination, hybridization, and both long-distance and localized clonal expansion in the global CGSC population.

Clonal Expansion in Multiple Phyllosticta Species Causing Citrus Black Spot or Similar Symptoms in China

“…Similar results have been reported for others citrus fungal pathogens like Diaporthe citri [58] and P. citriasiana [24]. Although sexual spores are often considered as the primary source of dispersal and infections [56,59], clonal expansion of specific genotypes has been reported in many pathogens, leading to serious disease epidemics [53,[60][61][62][63][64]. Examples of clonal expansion in fungal pathogens include the banana wilt, caused by Foc TR4 that has been reported across various regions in at least 17 countries in the world [53,61,62].…”

“…The most commercially harmful Phyllosticta disease to the citrus industry in China is black spot caused by P. citricarpa and P. paracitricarpa. Our results suggest that targeted markers should be developed to monitor the prevalence and spread of clonal genotypes in these species [53,64]. In addition, the highly prevalent genotypes should be further evaluated for their susceptibilities to fungicides and for their genomic features [60,61].…”

Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections

“…The patterns suggest the presence of unique and indigenous genetic diversity within Qatar, and that sexual mating and recombination among strains from divergent genetic clusters is not common. The presence of divergent lineages within the same geographical regions have been reported for several human fungal pathogens, including C. auris [86] and the human pathogenic Cryptococcus species complexes [89, 90]. In addition, the presence of divergent strains and clusters in both the Qatar and the global samples suggests historical genetic differentiations among subpopulations of C. glabrata .…”

“…Evidence for both recent short- and long-distance dispersals has been reported for C. glabrata and several other human fungal pathogens, including Aspergillus fumigatus [84, 85] , Candida auris [86], Candida albicans [87], Candida tropicalis [88] and multiple lineages within the human pathogenic Cryptococcus , including in both the Cryptococcus neoformans and Cryptococcus gattii species complexes [89, 90]. However, in most of these molecular epidemiological and population genetic studies of human fungal pathogens, few isolates were from the Middle East region, an ecologically distinct region with a hot climate.…”

Genetic structure and triazole resistance among Aspergillus fumigatus populations from remote and undeveloped regions in Eastern Himalaya

“…It has been suggested that free-living microbial eukaryotes smaller than 1–3 µM are highly mobile and can be effectively dispersed by wind over long distances; thus, blurring the potential effects of geographic separation on their genetic relationships ( 12 , 13 ). Though spores (e.g., asexual spores, ascospores, and basidiospores) of many fungi are in that size range and found cosmopolitan, an increasing number of fungal species showed significant contributions of geography, topography, climate oscillations, ecological, and physical barriers to their genetic variation, such as in Aspergillus ( 9 , 14 ), Cryptococcus ( 15 , 16 ), Neurospora ( 17 , 18 ), yeast ( 19 , 20 ), etc. In A. fumigatus , the effects on prominent local and regional landscape factors, such as steep mountains and deep gorges to genetic variations remain to be investigated.…”