Molecular Genetic Analyses of Mating Pheromones Reveal Intervariety Mating or Hybridization in Cryptococcus neoformans

ABSTRACT The sexual mating of the pathogenic yeast Cryptococcus neoformans is important for pathogenesis studies because the fungal virulence is linked to the α mating type (MATα). We characterized C. neoformans mating pheromones (MFα 1 and MFa1) from 122 strains to understand intervariety hybridization or mating and intervariety virulence. MFα 1 in three C. neoformans varieties showed (a) specific nucleotide polymorphisms, (b) different copy numbers and chromosomal localizations, and (c) unique deduced amino acids in two geographic populations of C. neoformans var. gattii. MFα 1 of different varieties cross-hybridized in Southern hybridizations. Their phylogenetic analyses showed purifying selection (neutral evolution). These observations suggested that MATα strains from any of the three C. neoformans varieties could mate or hybridize in nature with MAT a strains of C. neoformans var. neoformans. A few serotype A/D diploid strains provided evidence for mating or hybridization, while a majority of A/D strains tested positive for haploid MFα 1 identical to that of C. neoformans var. grubii. MFα 1 sequence and copy numbers in diploids were identical to those of C. neoformans var. grubii, while their MFa1 sequences were identical to those of C. neoformans var. neoformans; thus, these strains were hybrids. The mice survival curves and histological lesions revealed A/D diploids to be highly pathogenic, with pathogenicity levels similar to that of the C. neoformans var. grubii type strain and unlike the low pathogenicity levels of C. neoformans var. neoformans strains. In contrast to MFα 1 in three varieties, MFa1 amplicons and hybridization signals could be obtained only from two C. neoformans var. neoformans reference strains and eight A/D diploids. This suggested that a yet undiscovered MFa pheromone(s) in C. neoformans var. gattii and C. neoformans var. grubii is unrelated to, highly divergent from, or rarer than that in C. neoformans var. neoformans. These observations could form the basis for future studies on the role of intervariety mating in C. neoformans biology and virulence.

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Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma

Genome Biology and Evolution ◽

10.1093/gbe/evz214 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2909-2916 ◽

Cited By ~ 1

Author(s):

Qi Liu ◽

Deng Lin ◽

Mingkun Li ◽

Zhenglong Gu ◽

Yiqiang Zhao

Keyword(s):

Hepatocellular Carcinoma ◽

Mitochondrial Dna ◽

Nuclear Genome ◽

Purifying Selection ◽

Neutral Evolution ◽

Single Nucleotide Variants ◽

Copy Numbers ◽

Nontumor Tissue ◽

Mtdna Diversity ◽

Single Tumor

Abstract Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.

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Phagocytosis of Cryptococcus neoformans by, and Nonlytic Exocytosis from, Acanthamoeba castellanii

Applied and Environmental Microbiology ◽

10.1128/aem.00812-10 ◽

2010 ◽

Vol 76 (18) ◽

pp. 6056-6062 ◽

Cited By ~ 53

Author(s):

Cara J. Chrisman ◽

Mauricio Alvarez ◽

Arturo Casadevall

Keyword(s):

Cryptococcus Neoformans ◽

Virulence Factors ◽

Acanthamoeba Castellanii ◽

Wild Type ◽

Pathogenic Yeast ◽

Fungal Virulence ◽

Environmental Interactions ◽

Soil Amoeba ◽

Additional Support ◽

Mammalian Infection

ABSTRACT Cryptococcus neoformans, an encapsulated, pathogenic yeast, is endowed with a variety of virulence factors, including a polysaccharide capsule. During mammalian infection, the outcome of the interaction between C. neoformans and macrophages is central to determining the fate of the host. Previous studies have shown similarities between the interaction of C. neoformans with macrophages and with amoebae, resulting in the proposal that fungal virulence for mammals originated from selection by amoeboid predators. In this study, we investigated the interaction of C. neoformans with the soil amoeba Acanthamoeba castellanii. Comparison of phagocytic efficiency of the wild type, nonencapsulated mutants, and complemented strains showed that the capsule was antiphagocytic for amoebae. Capsular enlargement was associated with a significant reduction in phagocytosis, suggesting that this phenomenon protects against ingestion by phagocytic predators. C. neoformans var. neoformans cells were observed to exit amoebae several hours after ingestion, in a process similar to the recently described nonlytic exocytosis from macrophages. Cryptococcal exocytosis from amoebae was dependent on the strain and on actin and required fungal viability. Additionally, the presence of a capsule was inversely correlated with the likelihood of extrusion in certain strains. In summary, nonlytic exocytosis from amoebae provide another parallel to observations in fungus-macrophage interactions. These results provide additional support for the notion that some mechanisms of virulence observed during mammalian infection originated, and were selected for, by environmental interactions.

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A new hip-pocket frog from mid-eastern Australia (Anura: Myobatrachidae: Assa)

Zootaxa ◽

10.11646/zootaxa.5057.4.1 ◽

2021 ◽

Vol 5057 (4) ◽

pp. 451-486

Author(s):

MICHAEL J. MAHONY ◽

HARRY B. HINES ◽

STEPHEN V. MAHONY ◽

BEDE MOSES ◽

SARAH R. CATALANO ◽

...

Keyword(s):

Genetic Relationships ◽

Phylogenetic Analyses ◽

Molecular Genetic ◽

Nuclear Genome ◽

Critically Endangered ◽

Nominal Species ◽

Nucleotide Polymorphisms ◽

Conservation Assessment ◽

Separate Species ◽

Eastern Australia

The hip-pocket frog (Assa darlingtoni), a small terrestrial myobatrachid frog found in mid-eastern Australia, has a highly derived, unusual, reproductive mode involving a unique form of male parental care. Males have subcutaneous pouches that open near the hip, and the developing tadpoles are carried in these pouches to post metamorphosis. It is found on several isolated mountain ranges in closed forest habitats, associated with high rainfall and temperate or sub-tropical climates. We established genetic relationships among specimens sampled across the range using phylogenetic analyses of thousands of single nucleotide polymorphisms (SNPs) from the nuclear genome and mitochondrial ND2 gene nucleotide sequences. These analyses uncovered two lineages that are genetically distinct in both nDNA and mtDNA analyses and that have low levels of divergence in male advertisement calls and are morphologically cryptic. Our data support separate species status for each lineage, based on the molecular genetic data. The first, which we name as a new species, Assa wollumbin sp. nov., is restricted to a single mountain, Wollumbin (= Mount Warning), the eroded cone of an ancient shield volcano—the Tweed Volcano. The second, the nominal species A. darlingtoni, has a wider distribution in five geographically disjunct subpopulations along 430 km of the Great Dividing Range in south-eastern Queensland and north-eastern New South Wales. The distributions of the two species closely approach within 15 km of each other on the central plug and rim of the caldera of the Tweed Volcano. Assa wollumbin sp. nov. meets the conservation criteria for Critically Endangered [A3(e), B2(a,b)]. When all subpopulations of A. darlingtoni are combined the conservation assessment is Endangered [A3(e), B2(a,b)]. Because of the fragmented nature of the distribution of A. darlingtoni, combined with the genetic evidence of concordant sub-structuring, we also conducted a conservation assessment on the five subpopulations. Two were assessed as Critically Endangered (D’Aguilar Range and Conondale/Blackall Ranges), and the remainder as Endangered (Dorrigo Plateau, McPherson Ranges, and Gibraltar Ranges/Washpool).

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Faculty Opinions recommendation of Efficient implementation of RNA interference in the pathogenic yeast Cryptococcus neoformans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.10626956.11500054 ◽

2011 ◽

Author(s):

Jason Stajich

Keyword(s):

Rna Interference ◽

Cryptococcus Neoformans ◽

Efficient Implementation ◽

Pathogenic Yeast

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Faculty Opinions recommendation of Cryptococcus neoformans copper detoxification machinery is critical for fungal virulence.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717989863.793473057 ◽

2013 ◽

Author(s):

Guilhem Janbon

Keyword(s):

Cryptococcus Neoformans ◽

Fungal Virulence

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New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

Biotekhnologiya ◽

10.21519/0234-2758-2020-36-6-49-54 ◽

2020 ◽

Vol 36 (6) ◽

pp. 49-54

Author(s):

A.A. Nalbandyan ◽

T.P. Fedulova ◽

I.V. Cherepukhina ◽

T.I. Kryukova ◽

N.R. Mikheeva ◽

...

Keyword(s):

Sugar Beet ◽

Flowering Time ◽

Molecular Genetic ◽

Bioinformatic Analysis ◽

Early Flowering ◽

Nucleotide Polymorphisms ◽

Nucleotide Substitutions ◽

Time Control ◽

Flowering Time Control ◽

Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

Scientific Reports ◽

10.1038/s41598-021-90325-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kyung Seok Kim ◽

Kevin J. Roe

Keyword(s):

Phylogenetic Analyses ◽

Freshwater Mussel ◽

Conservation Strategies ◽

Nucleotide Polymorphisms ◽

Conservation Units ◽

Genetic Structuring ◽

The North ◽

Snp Data ◽

Genome Wide ◽

Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

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Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Evolutionary Bioinformatics ◽

10.1177/1176934319889948 ◽

2019 ◽

Vol 15 ◽

pp. 117693431988994

Author(s):

Shulin Zhang ◽

Yaling Cai ◽

Jinggong Guo ◽

Kun Li ◽

Renhai Peng ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs ◽

Association Analyses ◽

Genome Wide ◽

Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

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Comparative gene genealogical analyses of strains of serotype AD identify recombination in populations of serotypes A and D in the human pathogenic yeast Cryptococcus neoformans

Microbiology ◽

10.1099/mic.0.26180-0 ◽

2003 ◽

Vol 149 (8) ◽

pp. 2147-2154 ◽

Cited By ~ 38

Author(s):

Jianping Xu ◽

Thomas G. Mitchell

Keyword(s):

Monoclonal Antibodies ◽

Cryptococcus Neoformans ◽

Natural Populations ◽

The Other ◽

Pathogenic Yeast ◽

Gene Genealogy ◽

Serotype A ◽

The World ◽

Significant Divergence ◽

Allelic Group

Cryptococcus neoformans is a major pathogen of humans throughout the world. Using commercial monoclonal antibodies to capsular epitopes, strains of C. neoformans manifest five serotypes: A, B, C, D and AD. Previous studies demonstrated significant divergence among serotypes A, B, C and D, which are typically haploid. In contrast, most strains of serotype AD are diploid or aneuploid and result from recent hybridization between strains of serotypes A and D. Whether serotypes A, B, C and D represent strictly asexual lineages is not known. Using comparative genealogical analyses of two genes, the authors investigated whether recombination occurred among strains within serotypes A and D. For each of 14 serotype AD strains, a portion (642 bp) of the orotidine monophosphate pyrophosphorylase (URA5) gene was cloned and sequenced. Each of these 14 strains contained two different alleles and sequences for both alleles were obtained. The URA5 gene genealogy was compared to that derived from the laccase (LAC) gene, which was reported recently for the same 14 strains. For both genes, each of the 14 serotype AD strains contained two phylogenetically distinct alleles: one allele was highly similar to those from serotype A strains and the other to alleles from serotype D strains. However, within both the serotype A allelic group and the serotype D allelic group, there was significant incongruence between genealogies derived from URA5 and LAC. The results suggest recombination in natural populations of both serotypes A and D.

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