Analysis of the genome and transcriptome of [i]Cryptococcus neoformans[/i] var.[i] grubii[/i] reveals complex RNA expression and microevolution leading to virulence attenuation

Guilhem Janbon (1) , Kate L. Ormerod (2) , Damien Paulet (3) , Edmond J. Byrnes (4) , Vikas Yadav (5) , Gautam Chatterjee (5) , Nandita Mullapudi (6) , Chung-Chau Hon (7) , R. Blake Billmyre (4) , François Brunel (8) , Yong-Sun Bahn (9) , Weidong Chen (10) , Yuan Chen (4) , Eve W. L. Chow (2) , Jean-Yves Coppée (3) , Anna Floyd-Averette (4) , Claude Gaillardin (8) , Kimberly J. Gerik (11) , Jonathan Goldberg (12) , Sara Gonzalez-Hilarion (1) , Sharvari Gujja (12) , Joyce L. Hamlin (13) , Yen-Ping Hsueh (4, 14) , Giuseppe Ianiri (15) , Steven Jones (16) , Chinnappa D. Kodira (12) , Lukasz Kozubowski (17) , Woei Lam (11) , Marco Marra (16) , Larry D. Mesner (13) , Piotr A. Mieczkowski (18) , Frederique Moyrand (1) , Kirsten Nielsen (4, 19) , Caroline Proux (3) , Tristan Rossignol (8) , Jacqueline E. Schein (16) , Sheng Sun (4) , Carolin Wollschlaeger (1) , Ian A. Wood (20) , Qiandong Zeng (12) , Cécile Neuvéglise (8) , Carol S. Newlon (10) , John R. Perfect (4) , Jennifer K. Lodge (11) , Alexander Idnurm (15) , Jason E. Stajich (4, 21) , James W. Kronstad (22) , Kaustuv Sanyal (5) , Joseph Heitman (4) , James A. Fraser (2) , Christina A. Cuomo (12) , Fred S. Dietrich (4)

1 BPF - Biologie et Pathogénicité fongiques
2 School of Chemistry and Molecular Biosciences [Brisbane]
3 PF2 - Transcriptome et Epigénome
4 MGM - Department of Molecular Genetics and Microbiology [Durham]
5 JNCASR - Jawaharlal Nehru Centre for Advanced Scientific Research
6 Genotypic Technology Private Limited
7 Biologie Cellulaire du Parasitisme
8 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
9 Center for Fungal Pathogenesis, Department of Biotechnology [Yonsei]
10 Department of Microbiology and Molecular Genetics [Newark]
11 School of Medicine, Department of Molecular Microbiology [St. Louis]
12 BROAD INSTITUTE - Broad Institute of MIT and Harvard
13 Department of Biochemistry and Molecular Genetics [Charlottesville]
14 Division of Biology [Pasadena]
15 School of Biological Sciences, Division of Cell Biology and Biophysics [Kansas City]
16 CMSGSC - Canada's Michael Smith Genome Sciences Centre
17 Department of Genetics and Biochemistry [Clemson]
18 Department of Genetics [Chapel Hill]
19 Microbiology Department [Minneapolis]
20 School of Mathematics and Physics [Brisbane]
21 Department of Plant Pathology & Microbiology [Riverside]
22 UBC Microbiology - Department of Microbiology and Immunology [Vancouver]

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.

Domaines: Sciences du Vivant [q-bio]

Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, et al.. Analysis of the genome and transcriptome of [i]Cryptococcus neoformans[/i] var.[i] grubii[/i] reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genetics, 2014, 10 (4), ⟨10.1371/journal.pgen.1004261⟩. ⟨hal-01204377⟩