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.

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Citation

Published Version (Please cite this version)

10.1371/journal.pgen.1004261

Publication Info

Janbon, G, KL Ormerod, D Paulet, EJ Byrnes, V Yadav, G Chatterjee, N Mullapudi, C Hon, et al. (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). p. e1004261. 10.1371/journal.pgen.1004261 Retrieved from https://hdl.handle.net/10161/8468.

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Scholars@Duke

Yadav

Vikas Yadav

Research Associate, Senior
Lodge

Jennifer Lodge

Vice President for Research and Innovation

Jennifer Lodge, Ph.D., a professor of molecular genetics and microbiology, is Duke’s vice president for Research & Innovation.

As the university’s chief research and innovation officer, Lodge leads oversight of Duke’s $1.2 billion annual research portfolio, including grants administration, ethical practices and commercialization. Lodge works with campus and medical center research staff, faculty and trainees, and is a key figure in Duke’s connection with external partners.

Before coming to Duke in January 2022, Lodge served as vice chancellor for research and senior associate dean for research for the School of Medicine at Washington University in St. Louis (WUSTL). There, she was responsible for WUSTL’s research development, ethics, education, compliance and research administration systems, and earned a reputation for encouraging innovation and entrepreneurship.

Lodge’s own research is on the human pathogenic fungus Cryptococcus neoformans. Her lab has been funded continuously by NIH for more than two decades, with as many as three prestigious R01 grants at one time. Her lab in the Duke University School of Medicine continues to explore the biochemical processes by which this fungus builds its cell walls. Such knowledge could lead to new antifungal therapies and vaccines.

Lodge is a fellow of the American Academy of Microbiology, the American Association for the Advancement of Science (AAAS) and the National Academy of Inventors. She is also the former chair of the Group on Research at the American Association of Medical Colleges (AAMC).

Dietrich

Fred Samuel Dietrich

Associate Professor of Molecular Genetics and Microbiology

My laboratory is interested in fungal genomics.

In particular we use genomic sequencing of fungal strains and species in comparative analysis. Starting with the sequencing of Saccharomyces cerevisiae strain S288C, I have been involved in the genome sequencing and annotation of Ashbya gossypiiCryptococcus neoformans var. grubii and ~100 additional S. cerevisiae strains. We currently use Illumina paired end and mate paired sequencing, as this is at presently the most cost effective widely used technology capable of generating high accuracy, zero gap whole genome sequences. The 100-genomes S. cerevisiae data as well as the fully updated fully annotated A. gossypii sequence (Genbank numbers AE016814-AE016820), which spans all seven chromosomes from telomere to telomere, were generated using Illumina data. In my laboratory we strive to utilize comparative genomics data to understand aspects of basic fungal biology. Some of our specific areas of interest are filamentous growth, mapping of complex traits, horizontal gene transfer, and identification of RNA coding genes. This work involves a combination of experimental work and bioinformatics analysis. Research in S. cerevisiae has greatly benefitted from an accurate, annotated S. cerevisiae reference genome, and that research into the tremendous diversity in this organism will similarly benefit from the availability of a large number of accurate, fully annotated genome sequences. The use of genomic information to better understand the biology of these organisms, and this is what students in my laboratory generally work on.



What is the set of genes found in a pathogenic fungus such as Cryptococcus?

Our interest in this human pathogen is to expand beyond looking at one isolate and to investigate the diversity in the population. Are there genes found in some Cryptococcus neoformans isolates but not in others? Are there regions of the genome or individual genes which are highly diverged between Cryptococcus isolates? Efforts are now underway at Stanford University to sequence the genome of the JEC21 strain of Cryptococcus. This is a strain that has been agreed upon by the community of Cryptococcus researchers as a reference strain. Obtaining the DNA sequence of this strain is only the start however. From that sequence identifying the complete set of genes will be a considerable challenge requiring both bioinformatic as well as experimental tools. While this work on gene identification is going on we plan on addressing the question of how much do other Cryptococcus isolates differ from JEC21.

What is the set of genes in humans?

The complete DNA sequence of human and mouse will become available soon. This does not mean that we will know the complete set of human or mouse genes. Our current state of knowledge does not allow us to accurately predict human genes directly from DNA sequence. We are interested in applying to the human genome some of the experimental and bioinformatic tools we are developing and utilizing in fungal systems.

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