ArticlePLoS genetics2014
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
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Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 282 papers, 1 of them a synthesis that pooled it.
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282citing papers in PubMed, 1 pooled it
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Who cites it
282 citing papers in PubMed, 1 synthesis or guideline pooled it, 406 citations in OpenAlex.
- Single nucleotide polymorphisms are associated with strain-specific virulence differences among clinical isolates of Cryptococcus neoformans.Nature communications · 2024Pooled it
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- Mammalian-evolved strains of the fungal pathogen Cryptococcus neoformans show adaptation via heritable transcript level differences specific to mouse MHC haplotype.BMC genomics · 2026Article
- Decoding the genome of the basidiomycetous yeast Vishniacozyma victoriae D19: a promising fungal model for biotechnology.BMC genomics · 2026Article
- Neofunctionalization of H1 linker histones drives divergent gene expression and histone methylation in Cryptococcus neoformans.Communications biology · 2026Article
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- Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection.Molecular ecology resources · 2026Article
- The kinases Hsl101 and Urk1 regulate metabolism of Cryptococcus neoformans.Scientific reports · 2025Article
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- Vaccine-Mediated Protection of Mice Against African and Asian Clinical Strains ofJournal of fungi (Basel, Switzerland) · 2025Article
- Article
222 more citing papers are in PubMed but not listed here.
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Authors and funding
52 authors at 18 institutions in 6 countries.
Guilhem JanbonInstitut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
Kate L OrmerodUniversity of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
Damien PauletInstitut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France.
Edmond J ByrnesDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Vikas YadavJawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
Gautam ChatterjeeJawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
Nandita MullapudiGenotypic Technology Private Limited, Bangalore, India.
Chung-Chau HonInstitut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, Paris, France.
R Blake BillmyreDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
François BrunelINRA, UMR 1319 Micalis, Jouy-en-Josas, France.
Yong-Sun BahnYonsei University, Center for Fungal Pathogenesis, Department of Biotechnology, Seoul, Republic of Korea.
Weidong ChenRutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America.
Yuan ChenDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Eve W L ChowUniversity of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
Jean-Yves CoppéeInstitut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France.
Anna Floyd-AveretteDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Claude GaillardinINRA, UMR 1319 Micalis, Jouy-en-Josas, France.
Kimberly J GerikWashington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America.
Jonathan GoldbergBroad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Sara Gonzalez-HilarionInstitut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
Sharvari GujjaBroad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Joyce L HamlinUniversity of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America.
Yen-Ping HsuehDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America; California Institute of Technology, Division of Biology, Pasadena, California, United States of America.
Giuseppe IaniriUniversity of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America.
Steven JonesCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
Chinnappa D KodiraBroad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Lukasz KozubowskiClemson University, Department of Genetics and Biochemistry, Clemson, South Carolina, United States of America.
Woei LamWashington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America.
Marco MarraCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
Larry D MesnerUniversity of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America.
Piotr A MieczkowskiUniversity of North Carolina, Department of Genetics, Chapel Hill, North Carolina, United States of America.
Frédérique MoyrandInstitut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
Kirsten NielsenDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America; University of Minnesota, Microbiology Department, Minneapolis, Minnesota, United States of America.
Caroline ProuxInstitut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France.
Tristan RossignolINRA, UMR 1319 Micalis, Jouy-en-Josas, France.
Jacqueline E ScheinCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
Sheng SunDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Carolin WollschlaegerInstitut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
Ian A WoodUniversity of Queensland, School of Mathematics and Physics, Brisbane, Queensland, Australia.
Qiandong ZengBroad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Cécile NeuvégliseINRA, UMR 1319 Micalis, Jouy-en-Josas, France.
Carol S NewlonRutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America.
John R PerfectDuke University Medical Center, Duke Department of Medicine and Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Jennifer K LodgeWashington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America.
Alexander IdnurmUniversity of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America.
Jason E StajichDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America; University of California, Department of Plant Pathology & Microbiology, Riverside, California, United States of America.
James W KronstadMichael Smith Laboratories, Department of Microbiology and Immunology, Vancouver, British Columbia, Canada.
Kaustuv SanyalJawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
Joseph HeitmanDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
James A FraserUniversity of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
Christina A CuomoBroad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
Fred S DietrichDuke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
Duke Medical Center · USInstitut Pasteur · FRBroad Institute · USMicrobiologie de l’alimentation au service de la santé · FRThe University of Queensland · AUBC Cancer Agency · CAJawaharlal Nehru Centre for Advanced Scientific Research · INWashington University in St. Louis · USRutgers, The State University of New Jersey · USUniversity of Missouri–Kansas City · USUniversity of Virginia · USCalifornia Institute of Technology · USCanada's Michael Smith Genome Sciences Centre · CAClemson University · USUniversity of California, Riverside · USUniversity of Minnesota · USUniversity of North Carolina at Chapel Hill · USYonsei University · KR
Funding
Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6MORGANIZATION AND FUNCTIONS OF CELLULAR STRUCTUREST32GM007184 · NIGMS · DUKE UNIVERSITY · PI JINKS-ROBERTSON, SUE · 1985 to 2019
$18.2MTri-Institutional Molecular Mycology and Pathogenesis Training ProgramT32AI052080 · NIAID · DUKE UNIVERSITY · PI ANDREW ALSPAUGH, JOSEPH HEITMAN · 2003 to 2026
$8.7MStructure, function, and evolution of the Cryptococcus MAT locusR01AI050113 · NIAID · DUKE UNIVERSITY · PI HEITMAN, JOSEPH · 2002 to 2024
$8.5MGenetics Training Grant-Year 26T32GM007754 · NIGMS · DUKE UNIVERSITY · PI HAASE, STEVEN B · 1985 to 2019
$8.3MROLE OF CALCINEURIN IN C. NEOFORMANS MATING AND FRUITINGR01AI039115 · NIAID · DUKE UNIVERSITY · PI HEITMAN, JOSEPH · 1997 to 2025
$6.7MComparative and functional genomics of C. neoformansR01AI053721 · NIAID · UNIVERSITY OF BRITISH COLUMBIA · PI KRONSTAD, JAMES W · 2003 to 2024
$5.4MGenetics of Cryptococcus sexual reproductionR37AI039115 · NIAID · DUKE UNIVERSITY · PI HEITMAN, JOSEPH · 2011 to 2020
$4.9MPathobiology of C. neoformans in the Central Nervous SystemR01AI073896 · NIAID · DUKE UNIVERSITY · PI PERFECT, JOHN R. · 2008 to 2018
$4.4MEvolution of Cryptococcus neoformans Strains from Patients with HIV/AIDSR01AI093257 · NIAID · DUKE UNIVERSITY · PI PERFECT, JOHN R. · 2011 to 2022
$3.8MSignal transduction in C. neoformansR01AI050184 · NIAID · WASHINGTON UNIVERSITY · PI LODGE, JENNIFER K. · 2002 to 2012
$3.7MPheromones and Titan Cell Production in Cryptococcus neoformansR01AI080275 · NIAID · UNIVERSITY OF MINNESOTA · PI NIELSEN, KIRSTEN · 2011 to 2015
$1.8MNHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54HG003067NIAID NIH HHS AI094364NIAID NIH HHS AI39115-16NIAID NIH HHS AI50113-10NIAID NIH HHS HHSN272200900018CNIAID NIH HHS R01 AI039115NIAID NIH HHS R01 AI050113NIAID NIH HHS R01 AI050184NIAID NIH HHS R01 AI053721NIAID NIH HHS R01 AI073896NIAID NIH HHS R01 AI080275NIAID NIH HHS R01 AI093257NIAID NIH HHS R21 AI094364NIAID NIH HHS R37 AI039115NIAID NIH HHS T32 AI052080NIGMS NIH HHS T32 GM007184NIGMS NIH HHS T32 GM007754NINDS NIH HHS NS042263NINDS NIH HHS R01 NS042263
Abstract
Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.
Indexed as
Chromosomes, FungalCryptococcus neoformansDNA, FungalGenome, FungalIntronsRNA, FungalTranscriptomeVirulenceDNA, FungalRNA, Fungal
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