Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

M. Cogliati; P. E. Chidebelu; M. Hitchcock; M. Chen; V. Rickerts; S. Ackermann; M. Desnos Ollivier; J. Inácio; U. Nawrot; M. Florek; K. J. Kwon-Chung; D. H. Yang; C. Firacative; C. A. Puime; P. Escandon; S. Bertout; F. Roger; J. Xu

doi:10.1016/j.fgb.2023.103861

Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

M. Cogliati, P. E. Chidebelu, M. Hitchcock, M. Chen, V. Rickerts, S. Ackermann, M. Desnos Ollivier, J. Inácio, U. Nawrot, M. Florek, K. J. Kwon-Chung, D. H. Yang, C. Firacative, C. A. Puime, P. Escandon, S. Bertout, F. Roger, J. Xu

Research output: Contribution to journal › Article › peer-review

Abstract

Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.

Original language	English
Article number	103861
Journal	Fungal Genetics and Biology
Volume	170
DOIs	https://doi.org/10.1016/j.fgb.2023.103861
Publication status	Published - 19 Dec 2023

Keywords

AD hybrids
Cryptococcus neoformans
Loss of heterozygosity
MLST
Multiple origin
Phylogenetics

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Cogliati, M., Chidebelu, P. E., Hitchcock, M., Chen, M., Rickerts, V., Ackermann, S., Desnos Ollivier, M., Inácio, J., Nawrot, U., Florek, M., Kwon-Chung, K. J., Yang, D. H., Firacative, C., Puime, C. A., Escandon, P., Bertout, S., Roger, F., & Xu, J. (2023). Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids. Fungal Genetics and Biology, 170, Article 103861. https://doi.org/10.1016/j.fgb.2023.103861

@article{2f416a82b1724717be792d34a29054f5,

title = "Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids",

abstract = "Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.",

keywords = "AD hybrids, Cryptococcus neoformans, Loss of heterozygosity, MLST, Multiple origin, Phylogenetics",

author = "M. Cogliati and Chidebelu, {P. E.} and M. Hitchcock and M. Chen and V. Rickerts and S. Ackermann and {Desnos Ollivier}, M. and J. In{\'a}cio and U. Nawrot and M. Florek and Kwon-Chung, {K. J.} and Yang, {D. H.} and C. Firacative and Puime, {C. A.} and P. Escandon and S. Bertout and F. Roger and J. Xu",

year = "2023",

month = dec,

day = "19",

doi = "10.1016/j.fgb.2023.103861",

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Cogliati, M, Chidebelu, PE, Hitchcock, M, Chen, M, Rickerts, V, Ackermann, S, Desnos Ollivier, M, Inácio, J, Nawrot, U, Florek, M, Kwon-Chung, KJ, Yang, DH, Firacative, C, Puime, CA, Escandon, P, Bertout, S, Roger, F & Xu, J 2023, 'Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids', Fungal Genetics and Biology, vol. 170, 103861. https://doi.org/10.1016/j.fgb.2023.103861

TY - JOUR

T1 - Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

AU - Cogliati, M.

AU - Chidebelu, P. E.

AU - Hitchcock, M.

AU - Chen, M.

AU - Rickerts, V.

AU - Ackermann, S.

AU - Desnos Ollivier, M.

AU - Inácio, J.

AU - Nawrot, U.

AU - Florek, M.

AU - Kwon-Chung, K. J.

AU - Yang, D. H.

AU - Firacative, C.

AU - Puime, C. A.

AU - Escandon, P.

AU - Bertout, S.

AU - Roger, F.

AU - Xu, J.

PY - 2023/12/19

Y1 - 2023/12/19

N2 - Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.

AB - Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.

KW - AD hybrids

KW - Cryptococcus neoformans

KW - Loss of heterozygosity

KW - MLST

KW - Multiple origin

KW - Phylogenetics

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AN - SCOPUS:85180978086

SN - 1087-1845

VL - 170

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

M1 - 103861

ER -

Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

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Keywords

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