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Title: Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Authors: Janbon, Guilhem
Ormerod, Kate L.
Paulet, Damien
Byrnes, Edmond J., III
Yadav, Vikas
Chatterjee, Gautam
Mullapudi, Nandita
Hon, Chung-Chau
Billmyre, R. Blake
Brunel, Francois
Bahn, Yong-Sun
Chen, Weidong
Chen, Yuan
Chow, Eve W. L.
Coppee, Jean-Yves
Floyd-Averette, Anna
Gaillardin, Claude
Gerik, Kimberly J.
Goldberg, Jonathan
Gonzalez-Hilarion, Sara
Gujja, Sharvari
Hamlin, Joyce L.
Hsueh, Yen-Ping
Ianiri, Giuseppe
Jones, Steven
Kodira, Chinnappa D.
Kozubowski, Lukasz
Lam, Woei
Marra, Marco
Mesner, Larry D.
Mieczkowski, Piotr A.
Moyrand, Frederique
Nielsen, Kirsten
Proux, Caroline
Rossignol, Tristan
Schein, Jacqueline E.
Sun, Sheng
Wollschlaeger, Carolin
Wood, Ian A.
Zeng, Qiandong
Neuveglise, Cecile
Newlon, Carol S.
Perfect, John R.
Lodge, Jennifer K.
Idnurm, Alexander
Stajich, Jason E.
Kronstad, James W.
Sanyal, Kaustuv
Heitman, Joseph
Fraser, James A.
Cuomo, Christina A.
Dietrich, Fred S.
Keywords: Genetics & Heredity
DNA-Sequencing Data
Replication Origins
Alternative Polyadenylation
Seq Data
Nucleotide Resolution
Functional Genomics
Centromere Function
Gene Prediction
Sexual Cycle
Issue Date: 2014
Publisher: Public Library of Science
Citation: Janbon, G; Ormerod, KL; Paulet, D; Byrnes, EJ; Yadav, V; Chatterjee, G; Mullapudi, N; Hon, CC; Billmyre, RB; Brunel, F; Bahn, YS; Chen, WD; Chen, Y; Chow, EWL; Coppee, JY; Floyd-Averette, A; Gaillardin, C; Gerik, KJ; Goldberg, J; Gonzalez-Hilarion, S; Gujja, S; Hamlin, JL; Hsueh, YP; 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, QD; Neuveglise, 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 Genetics 2014, 10 (4), e1004261
PLoS Genetics
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.
Description: Open Access
ISSN: 1553-7390
Appears in Collections:Research Papers (Kaustuv Sanyal)

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