Data from: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating-type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans. Input file for StructureInput file for Structure. 139 isolates in total without two VNII isolates.Structure.inputInput file for SplitsTreeInput file for SplitsTreeSplitsTree.nexInput file for SmartPCAInput file for SmartPCASmartPCA.pedInput file for MultiLocInput file for MultiLocMultiloc.musInput file for eBurstInput file for eBurstEBurst.csvConcatenated fasta fileConcatenated fasta file of all isolates with 8 loci.Concatenate.all.fasAligned fasta file of CAP59CAP59.all.noRef.aln.fasAligned fasta file of GPD1GPD1.all.noRef.aln.fasAligned fasta file of IGS1IGS1.all.noRef.aln.fasAligned fasta file of LAC1LAC1.all.noRef.aln.fasAligned fasta file of PLB1PLB1.all.noRef.aln.fasAligned fasta file of SOD1SOD1.all.noRef.aln.fasAligned fasta file of TEF1TEF1.all.noRef.aln.fasAligned fasta file of URA5URA5.all.noRef.aln.fasPacBio CCS ReadsPacbio CCS raw reads, barcode information and primer sequences were used in MLSTEZ for generating consensus sequences.RawReads.zip