The Genome of the Basidiomycetous Yeast and Human Pathogen
            <i>Cryptococcus neoformans</i>

Loftus, Brendan J.; Fung, Eula; Roncaglia, Paola; Rowley, Don; Amedeo, Paolo; Bruno, Dan; Vamathevan, Jessica; Miranda, Molly; Anderson, Iain; Fraser, James A.; Allen, Jonathan; Bosdet, Ian; Brent, Michael R.; Chiu, Readman; Doering, Tamara L.; Donlin, Maureen J.; D’Souza, Cletus A.; Fox, Donald T.; Grinberg, V.B.; Fu, Jianmin; Fukushima, Marilyn; Haas, Brian J.; Huang, Jen‐Yu; Janbon, Guilhem; Jones, Steven J.M.; Koo, Hean; Krzywinski, Martin; Kwon‐Chung, June; Lengeler, Klaus B.; Maiti, Rama; Marra, Marco A.; Marra, Robert E.; Mathewson, Carrie; Mitchell, Thomas G.; Pertea, Mihaela; Riggs, Florenta; Salzberg, Steven L.; Schein, Jacqueline E.; Shvartsbeyn, Alla; Shin, Heesun; Shumway, Martin; Specht, Charles A.; Suh, Bernard; Tenney, Aaron; Utterback, Terry; Wickes, Brian L.; Wortman, Jennifer; Wye, Natasja; Kronstad, James W.; Lodge, Jennifer K.; Heitman, Joseph; Davis, Ronald W.; Fraser, Claire M.; Hyman, Richard W.

doi:10.1126/science.1103773

Cited by 661 publications

(544 citation statements)

References 12 publications

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“…This suggests that an independent gene duplication event occurred in C. neoformans. Since the genome of C. neoformans was not duplicated during evolution (Loftus et al 2005), chromosomal translocation and segmental duplication processes might have resulted in the duplication of the -CAs. Only recently has the crystal structure of C. neoformans Can2 revealed that the enzyme belongs to the plant-type -CAs (Schlicker et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Evolution of carbonic anhydrases in fungi

Elleuche

Pöggeler

2009

Curr Genet

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Section: Discussionmentioning

confidence: 99%

Evolution of carbonic anhydrases in fungi

Elleuche

Pöggeler

2009

Curr Genet

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“…Schizophyllum commune has been reported as the causative agent of maxillary sinus infection (Kern and Uecker, 1986) and Cryptococcus neoformans is a well-studied fungal pathogen (Loftus et al, 2005) that causes life-threatening meningitis in immunocompromised patients (Mitchell and Perfect, 1995). Schizophyllum and Cryptococcus were concentrated in different particle-size ranges, d a o4.7 mm and d a 44.7 mm, respectively, and Schizophyllum was most abundant in the spring (Figure 2).…”

Section: Abundance Of Allergenic and Pathogenic Fungimentioning

confidence: 99%

Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air

et al. 2012

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Fungi are ubiquitous in outdoor air, and their concentration, aerodynamic diameters and taxonomic composition have potentially important implications for human health. Although exposure to fungal allergens is considered a strong risk factor for asthma prevalence and severity, limitations in tracking fungal diversity in air have thus far prevented a clear understanding of their human pathogenic properties. This study used a cascade impactor for sampling, and quantitative real-time PCR plus 454 pyrosequencing for analysis to investigate seasonal, size-resolved fungal communities in outdoor air in an urban setting in the northeastern United States. From the 20 libraries produced with an average of ∼800 internal transcribed spacer (ITS) sequences (total 15 326 reads), 12 864 and 11 280 sequences were determined to the genus and species levels, respectively, and 558 different genera and 1172 different species were identified, including allergens and infectious pathogens. These analyses revealed strong relationships between fungal aerodynamic diameters and features of taxonomic compositions. The relative abundance of airborne allergenic fungi ranged from 2.8% to 10.7% of total airborne fungal taxa, peaked in the fall, and increased with increasing aerodynamic diameter. Fungi that can cause invasive fungal infections peaked in the spring, comprised 0.1–1.6% of fungal taxa and typically increased in relative abundance with decreasing aerodynamic diameter. Atmospheric fungal ecology is a strong function of aerodynamic diameter, whereby through physical processes, the size influences the diversity of airborne fungi that deposit in human airways and the efficiencies with which specific groups of fungi partition from outdoor air to indoor environments.

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“…The most striking pattern is that of C. neoformans, which shows a very strong deletion bias (62% of all polymorphisms are deletions). If deletion/insertion bias predicts the direction of genome size evolution (Mira et al 2001), then C. neoformans may be in the process of a genome size reduction, although current gene density is not especially high (Loftus et al 2005).…”

Section: Mutational Spectrum Of the Rdna Polymorphismsmentioning

confidence: 99%

“…However, C. neoformans grows as a yeast and is a severe pathogen of immunocompromised humans. The haploid genome sequence was recently completed by the Stanford Genome Technology Center (Loftus et al 2005) (http://wwwsequence.stanford.edu/group/C.neoformans/index.html).…”

mentioning

confidence: 99%

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

Ganley¹,

Kobayashi²

2007

Genome Res.

328

268

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Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.[Supplemental material is available online at www.genome.org.]Repetitive elements are an abundant feature of genomes (Britten and Kohne 1968) and play critical roles in cell biology, genome structure, and adaptive evolution (Andersson et al. 1998;Shapiro and von Sternberg 2005). In many cases, repeats from a repeat family are highly similar to one another within a genome, a pattern that persists through evolutionary time even though sequence differences are apparent between species (Brown et al. 1972). Thus, the repeats seem to be maintained as a coherent family. This pattern is contrary to the expectations of conventional evolution, where repeats are expected to evolve independently ( Fig. 1) and diverge with time. This unusual mode of evolution, where repeats within a genome are more similar to each other than they are to "orthologous" repeats in a related species, is defined as concerted evolution (Zimmer et al. 1980). The molecular process responsible for concerted evolution is known as homogenization (Dover 1982), and although not fully elucidated, is thought to involve continual turnover of repeat copies by unequal recombination (e.g., Smith 1973;Szostak and Wu 1980;Kobayashi et al. 1998). However, recent studies have shown that several repeat families previously thought to evolve by concerted evolution actually evolve via a different evolutionary process known as birth-...

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The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans

Cited by 661 publications

References 12 publications

Evolution of carbonic anhydrases in fungi

Evolution of carbonic anhydrases in fungi

Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

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