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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...pathogenic fungi with large regional type centromeres, such as the closely related stem rust fungus Puccinia graminis f. sp. tritici (Sperschneider et al. 2021), a human pathogenic yeast Cryptococcus neoformans (Yadav et al. 2018b), and an ascomycetous phytopathogen Verticillium dahliae (Seidl et al. 2020...
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Resource: A fine scale phenotype–genotype virulence map of a bacterial pathogen
- Tim van Opijnen and
- Andrew Camilli
Genome Res. December 2012 22: 2541-2551; Published in Advance July 23, 2012, doi:10.1101/gr.137430.112
...Camilli A Camilli Camilli Andrew Tim van Opijnen Tim vanOpijnen Andrew, Camilli van Opijnen, T van Opijnen, Tim Camilli, A Andrew Tim van Opijnen van Opijnen Tim Tim, van Opijnen 10.1101/gr.137430.112 genome;gr.137430.112 1088-9051 A fine scale phenotype–genotype virulence map of a bacterial pathogen...
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RESOURCE: Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans
- Jacqueline E. Schein,
- Kristin L. Tangen,
- Readman Chiu,
- Heesun Shin,
- Klaus B. Lengeler,
- William Kim MacDonald,
- Ian Bosdet,
- Joseph Heitman,
- Steven J.M. Jones,
- Marco A. Marra,
- and James W. Kronstad
Genome Res. September 1, 2002 12: 1445-1453; Published in Advance August 21, 2002, doi:10.1101/gr.81002
...Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans Jacqueline E. Schein 1 , 4 , Kristin L. Tangen 2 , 4 , Readman Chiu 1 , Heesun Shin 1 , Klaus B. Lengeler 3 , William Kim...
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PERSPECTIVE: Genomics of the fungal kingdom: Insights into eukaryotic biology
- James E. Galagan,
- Matthew R. Henn,
- Li-Jun Ma,
- Christina A. Cuomo,
- and Bruce Birren
Genome Res. December 2005 15: 1620-1631; doi:10.1101/gr.3767105
...opportunity to study the biology and evolution of this medically, industrially, and environmentally important kingdom. In addition, fungi also serve as model organisms for all eukaryotes. The available fungal genomic resource, coupled with the experimental tractability of the fungi, is accelerating research...
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Resource: The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Pooja K. Strope,
- Daniel A. Skelly,
- Stanislav G. Kozmin,
- Gayathri Mahadevan,
- Eric A. Stone,
- Paul M. Magwene,
- Fred S. Dietrich,
- and John H. McCusker
Genome Res. May 2015 25: 762-774; Published in Advance April 3, 2015, doi:10.1101/gr.185538.114
...The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen Pooja K. Strope 1 , Daniel A. Skelly 2 , Stanislav G. Kozmin 1 , Gayathri Mahadevan 1...
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Article: Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- Laurence Despons,
- Cécile Fairhead,
- Gilles Fischer,
- Ingrid Lafontaine,
- Véronique Leh,
- Marc Lemaire,
- Jacky de Montigny,
- Cécile Neuvéglise,
- Agnès Thierry,
- Isabelle Blanc-Lenfle,
- Claudine Bleykasten,
- Julie Diffels,
- Emilie Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
...—Denver, Anschutz Medical Campus, Mail Stop 8101, P.O. Box 6511, Aurora, Colorado 80045, USA Abstract Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...mechanisms, including TE mobilization or homologous repair following DNA-double-stranded breaks (Todd et al. 2019, Berdan et al. 2021).The human fungal pathogen Candida albicans is an asexual diploid organism that displays significant genomic plasticity (Vande Zande et al. 2023). SVs are important drivers...
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Research: Genetic and phenotypic intra-species variation in Candida albicans
- Matthew P. Hirakawa,
- Diego A. Martinez,
- Sharadha Sakthikumar,
- Matthew Z. Anderson,
- Aaron Berlin,
- Sharvari Gujja,
- Qiandong Zeng,
- Ethan Zisson,
- Joshua M. Wang,
- Joshua M. Greenberg,
- Judith Berman,
- Richard J. Bennett,
- and Christina A. Cuomo
Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
...is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number...
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Research: Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
- Samuel M. Lancaster,
- Celia Payen,
- Caiti Smukowski Heil,
- and Maitreya J. Dunham
Genome Res. October 2019 29: 1685-1692; Published in Advance September 23, 2019, doi:10.1101/gr.245605.118
...their parental species (e.g., Stelkens et al. 2014), show desirable properties as industrial organisms (Mertens et al. 2015; Peris et al. 2017), and contribute to the emergence of fungal pathogens (Morales and Dujon 2012; Pryszcz et al. 2015; Schröder et al. 2016; Mixão and Gabaldón 2018). A whole- duplication...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...evolution in the C. parapsilosis clade. Unexpectedly, we found that the locations are different in two different C. parapsilosis isolates that we examined.ResultsIdentification of centromeres in C. parapsilosisMany fungal centromeres are located in large intergenic regions and may be flanked by IR sequences...
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