Dataset Information

Characterization and phylogenetic analysis of the complete mitochondrial genome of the human pathogenic fungus Cryptococcus sp. (Tremellales: Cryptococcaceae).

ABSTRACT: In the present study, the complete mitogenome of Cryptococcus sp. were sequenced and assembled. The complete mitogenome of Cryptococcus sp. was composed of circular DNA molecules, with a total length of 30,029?bp. The base composition of this mitochondrial genome is as follows: A (31.94%), T (34.89%), G (15.97%), and C (17.21%). The mitogenome contains 20 protein-coding genes, 2 ribosomal RNA genes (rRNA), and 22 transfer RNA (tRNA) genes. Phylogenetic analysis showed that the mitogenome of the Cryptococcus sp. exhibited a closest relationship with Cryptococcus gattii.

SUBMITTER: Chen Y

PROVIDER: S-EPMC7707753 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Characterization and phylogenetic analysis of the complete mitochondrial genome of the human pathogenic fungus Cryptococcus sp. (Tremellales: Cryptococcaceae).

Chen Yue Y Sun Xiaorong X Gui Wenjuan W Zhang Qianru Q Su Dan D

Mitochondrial DNA. Part B, Resources 20191121 2

In the present study, the complete mitogenome of Cryptococcus sp. were sequenced and assembled. The complete mitogenome of Cryptococcus sp. was composed of circular DNA molecules, with a total length of 30,029 bp. The base composition of this mitochondrial genome is as follows: A (31.94%), T (34.89%), G (15.97%), and C (17.21%). The mitogenome contains 20 protein-coding genes, 2 ribosomal RNA genes (rRNA), and 22 transfer RNA (tRNA) genes. Phylogenetic analysis showed that the mito ...[more]

PMID: 33366382

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Project description:The Cryptococcus complex consists of at least seven evolutionary divergent lineages and causes ∼200,000 fatal human infections each year worldwide. The dominant lineage is Cryptococcus neoformans which consists of three haploid clades VNI, VNII, and VNB, their haploid hybrids, and various diploids derived from intra- and inter-clade mating events. In this study, we analyzed the mitogenomes of 184 strains of C. neoformans. Our analyses revealed that all 184 mitogenomes contained the same 15 protein-coding genes in the same gene order. However, their mitogenome sizes varied between 24,740 and 31,327 bp, primarily due to differences in the number and size of mitochondrial introns. Twelve nucleotide sites within five mitochondrial genes were found to contain introns in at least one of the 184 strains, ranging from 2 to 7 introns within each mitogenome. The concatenated mitochondrial exon sequences of the 15 protein-coding genes and two rRNA genes showed that VNI, VNII, and VNB strains were separated into distinct clades or sub-clades, largely consistent with results based on nuclear genome SNPs. However, several novel findings were observed. First, one strain of the VNB clade contained mitogenome exon sequences identical to the main VNI mitogenome type but was distant to other VNB mitogenomes. Second, hybrids among clades VNI, VNII, and VNB identified based on their nuclear genome SNPs contained mitogenomes from different clades, with evidence of their mitogenomes inherited from either the MAT a or the MAT α parents. Third, the eight diploid VNB (C. neoformans) × VNIV (C. deneoformans) hybrids contained recombinant mitogenomes. Fourth, analyses of intron distribution and the paired exon-intron phylogenies for each of the 12 exon-intron pairs suggested frequent gains and losses of mitochondrial introns during the evolution of C. neoformans. The combined mitogenome exon-based phylogeny and intron distributions suggested that clades VNI, VNII and VNB could be further divided into sub-clades. Together, our results revealed a dynamic evolution of mitochondrial genomes in this important human fungal pathogen.

Project description:The basidiomycetous yeasts Cryptococcus neoformans and Cryptococcus gattii are closely related sibling species that cause respiratory and neurological disease in humans and animals. Within these two recognized species, phylogenetic analysis reveals at least six cryptic species defined as molecular types (VNI/II/B, VNIV, VGI, VGII, VGIII, and VGIV) that comprise the pathogenic Cryptococcus species complex. These pathogenic species are clustered in the Filobasidiella clade within the order Tremellales. Previous studies have shown that the Filobasidiella clade also includes several saprobic fungi isolated from insect frass, but information evaluating the relatedness of the saprobes and pathogens within this cluster is limited. Here, the phylogeny encompassing a subset of species in the Tremellales lineage that clusters closely with the pathogenic Cryptococcus species complex was resolved by employing a multilocus sequencing approach for phylogenetic analysis. Six highly conserved genomic loci from 15 related basidiomycete species were sequenced, and the alignments from the concatenated gene sequences were evaluated with different tree-building criteria. Furthermore, these 15 species were subjected to virulence and phenotype assays to evaluate their pathogenic potential. These studies revealed that Cryptococcus amylolentus and Tsuchiyaea wingfieldii, two nonpathogenic sibling species, are the taxa most closely related to the pathogens C. neoformans and C. gattii and together with Filobasidiella depauperata form a Cryptococcus sensu stricto group. Five other saprobic yeast species form the Kwoniella clade, which appears to be a part of a more distantly related sensu lato group. This study establishes a foundation for future comparative genomic approaches that will provide insight into the structure, function, and evolution of the mating type locus, the transitions in modes of sexual reproduction, and the emergence of human pathogenic species from related or ancestral saprobic species.

Dataset Information

Characterization and phylogenetic analysis of the complete mitochondrial genome of the human pathogenic fungus Cryptococcus sp. (Tremellales: Cryptococcaceae).

Publications

Characterization and phylogenetic analysis of the complete mitochondrial genome of the human pathogenic fungus <i>Cryptococcus</i> sp. (Tremellales: Cryptococcaceae).

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