title: Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
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.
authors.affiliation: Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
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authors.affiliation: University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
authors.forename: Kate L
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authors.lastname: Ormerod
authors.affiliation: Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France.
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authors.lastname: Paulet
authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: Edmond J
authors.initials: EJ
authors.lastname: Byrnes
authors.affiliation: Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
authors.forename: Vikas
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authors.lastname: Yadav
authors.affiliation: Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
authors.forename: Gautam
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authors.lastname: Chatterjee
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authors.affiliation: Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, Paris, France.
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authors.initials: CC
authors.lastname: Hon
authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: R Blake
authors.initials: RB
authors.lastname: Billmyre
authors.affiliation: INRA, UMR 1319 Micalis, Jouy-en-Josas, France.
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authors.lastname: Brunel
authors.affiliation: Yonsei University, Center for Fungal Pathogenesis, Department of Biotechnology, Seoul, Republic of Korea.
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authors.affiliation: Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America.
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authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
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authors.affiliation: University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
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authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
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authors.lastname: Gujja
authors.affiliation: University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America.
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authors.initials: YP
authors.lastname: Hsueh
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authors.affiliation: Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina, United States of America.
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authors.affiliation: University of Virginia, Department of Biochemistry and Molecular Genetics, Charlottesville, Virginia, United States of America.
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authors.initials: PA
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authors.forename: Frédérique
authors.initials: F
authors.lastname: Moyrand
authors.affiliation: Duke 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.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Nielsen
authors.affiliation: Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Paris, France.
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authors.affiliation: INRA, UMR 1319 Micalis, Jouy-en-Josas, France.
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authors.lastname: Rossignol
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
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authors.initials: JE
authors.lastname: Schein
authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: Sheng
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authors.lastname: Sun
authors.affiliation: Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
authors.forename: Carolin
authors.initials: C
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authors.affiliation: University of Queensland, School of Mathematics and Physics, Brisbane, Queensland, Australia.
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authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
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authors.affiliation: INRA, UMR 1319 Micalis, Jouy-en-Josas, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Neuvéglise
authors.affiliation: Rutgers New Jersey Medical School, Department of Microbiology and Molecular Genetics, Newark, New Jersey, United States of America.
authors.forename: Carol S
authors.initials: CS
authors.lastname: Newlon
authors.affiliation: Duke University Medical Center, Duke Department of Medicine and Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: John R
authors.initials: JR
authors.lastname: Perfect
authors.affiliation: Washington University School of Medicine, Department of Molecular Microbiology, St. Louis, Missouri, United States of America.
authors.forename: Jennifer K
authors.initials: JK
authors.lastname: Lodge
authors.affiliation: University of Missouri-Kansas City, School of Biological Sciences, Division of Cell Biology and Biophysics, Kansas City, Missouri, United States of America.
authors.forename: Alexander
authors.initials: A
authors.lastname: Idnurm
authors.affiliation: Duke 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.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Stajich
authors.affiliation: Michael Smith Laboratories, Department of Microbiology and Immunology, Vancouver, British Columbia, Canada.
authors.forename: James W
authors.initials: JW
authors.lastname: Kronstad
authors.affiliation: Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Biology and Genetics Unit, Bangalore, India.
authors.forename: Kaustuv
authors.initials: K
authors.lastname: Sanyal
authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: Joseph
authors.initials: J
authors.lastname: Heitman
authors.affiliation: University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia.
authors.forename: James A
authors.initials: JA
authors.lastname: Fraser
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Cuomo
authors.affiliation: Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America.
authors.forename: Fred S
authors.initials: FS
authors.lastname: Dietrich
mesh_terms: D015825:Chromosomes, Fungal / Q000235:genetics; D003455:Cryptococcus neoformans / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D007438:Introns / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D014774:Virulence / Q000235:genetics*
chemical_list: D004271:DNA, Fungal; D012331:RNA, Fungal
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