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

Publication ,  Journal Article
Janbon, G; Ormerod, KL; Paulet, D; Byrnes, EJ; Yadav, V; Chatterjee, G; Mullapudi, N; Hon, C-C; Billmyre, RB; Brunel, F; Bahn, Y-S; Chen, W ...
Published in: PLoS Genet
April 2014

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.

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Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

April 2014

Volume

10

Issue

4

Start / End Page

e1004261

Location

United States

Related Subject Headings

  • Virulence
  • Transcriptome
  • RNA, Fungal
  • Introns
  • Genome, Fungal
  • Developmental Biology
  • DNA, Fungal
  • Cryptococcus neoformans
  • Chromosomes, Fungal
  • 3105 Genetics
 

Citation

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Janbon, G., Ormerod, K. L., Paulet, D., Byrnes, E. J., Yadav, V., Chatterjee, G., … Dietrich, F. S. (2014). Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet, 10(4), e1004261. https://doi.org/10.1371/journal.pgen.1004261
Janbon, Guilhem, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, et al. “Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.PLoS Genet 10, no. 4 (April 2014): e1004261. https://doi.org/10.1371/journal.pgen.1004261.
Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, et al. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014 Apr;10(4):e1004261.
Janbon, Guilhem, et al. “Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.PLoS Genet, vol. 10, no. 4, Apr. 2014, p. e1004261. Pubmed, doi:10.1371/journal.pgen.1004261.
Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon C-C, Billmyre RB, Brunel F, Bahn Y-S, Chen W, Chen Y, Chow EWL, Coppée J-Y, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh Y-P, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014 Apr;10(4):e1004261.

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

April 2014

Volume

10

Issue

4

Start / End Page

e1004261

Location

United States

Related Subject Headings

  • Virulence
  • Transcriptome
  • RNA, Fungal
  • Introns
  • Genome, Fungal
  • Developmental Biology
  • DNA, Fungal
  • Cryptococcus neoformans
  • Chromosomes, Fungal
  • 3105 Genetics