Nothing Special in the Specialist? Draft Genome Sequence of Cryomyces antarcticus, the Most Extremophilic Fungus from Antarctica

Sterflinger, Katja; Lopandić, Ksenija; Pandey, Ram Vinay; Blasi, Barbara; Kriegner, Albert

doi:10.1371/journal.pone.0109908

Cited by 23 publications

(14 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The analysis suggested that the genome of C. antarcticus is very similar in size, content and composition to the other black fungi considered. These results imply that either all these diverse environments impose similar ecological challenges for black fungi (for instance, low water activity or high irradiation), that their adaptations are useful in a wide range of conditions, or that their peculiarities might be mediated by uncharacterized mechanisms (Sterflinger et al, ). However, since their polyextremophilic properties emerge due to accumulation of chemical compounds and control of universal traits such as membrane fluidity, phenotypic variation should be easy without extensive genomic innovation.…”

Section: Black Fungimentioning

confidence: 98%

“…Whole‐genome duplication might be an important evolutionary step allowing adaptation to highly specialized extreme niches, although to date Hortaea remains the only described example. One of the first comparative studies of black fungi involved the sequencing of the psychrophylic Cryomyces antarcticus (Dothideomycetes incertae sedis ) (Sterflinger et al, ). They compared C. antarcticus with several species of black fungi isolated from diverse environments.…”

Section: Black Fungimentioning

confidence: 99%

See 1 more Smart Citation

Fungal evolution: major ecological adaptations and evolutionary transitions

2019

View full text Add to dashboard Cite

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.

show abstract

Section: Black Fungimentioning

confidence: 98%

Section: Black Fungimentioning

confidence: 99%

Fungal evolution: major ecological adaptations and evolutionary transitions

2019

View full text Add to dashboard Cite

show abstract

“…The assembly completeness was also analyzed with Benchmarking Universal Single Copy Orthologs (BUSCO 3.0.1; Waterhouse et al 2017). In addition, 238 whole-genome assemblies of other Dothideomycetes were downloaded from NCBI Gen-Bank and the JGI Genome portal (Additional file 1: Table S1; Galagan et al 2005;Fedorova et al 2008;Sharpton et al 2009;Ellwood et al 2010;Desjardins et al 2011;Goodwin et al 2011;Rouxel et al 2011;Stukenbrock et al 2011;Chan et al 2012;Hu et al 2012;Joardar et al 2012;Ng et al 2012;Ohm et al 2012;Spatafora et al 2012;Blanco-Ulate et al 2013;Condon et al 2013;Lenassi et al 2013;Yew et al 2013;Aragona et al 2014;Bihon et al 2014;Chan et al 2014;Cooke et al 2014;Gao et al 2014;Gostinčar et al, 2014;Han et al 2014;Soliai et al 2014;Sterflinger et al 2014;van der Nest et al 2014;Yang et al 2014;Franco et al 2015;Grandaubert et al 2015;Kuan et al 2015;Morales-Cruz et al 2015;Orner et al 2015;Shaw et al 2015;Shiller et al 2015;…”

Section: Bioinformaticsmentioning

confidence: 99%

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

et al. 2019

View full text Add to dashboard Cite

Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

show abstract

“…Signi cant ndings from studies in these organisms include the stimulation of growth of some fungi by low dose IR [20][21][22]; the possibility that melanin in the cell walls of certain fungi can protect against IR through shielding, free-radical scavenging, or a physiological mechanism [21,23]; the high IR resistance of organisms such as Ustilago maydis [24][25][26][27], Cryptococcus neoformans [19,23,28,29], Cryomyces antarcticus [30], and Exophiala dermatitidis [31]; and the discovery of novel IR-resistanceassociated proteins through transcriptomics and targeted mutagenesis [19,28,31]. A portion of the radioresistance of fungi can be explained by their genome size, which is approximately two orders of magnitude smaller than mammals, and therefore sustains less damage per unit dose of IR, but within fungi there is also considerable variation in resistance that is not explained by genome size or composition (for instance, see [12,[31][32][33]).…”

mentioning

confidence: 99%

The transcriptomic and phenotypic response of the melanized yeast Exophiala dermatitidis to ionizing particle exposure

Schultzhaus

Chen

Shuryak

et al. 2020

Preprint

View full text Add to dashboard Cite

Fungi can tolerate extremely high doses of ionizing radiation compared with most other eukaryotes, a phenomenon encompassing both the recovery from acute exposure and the growth of melanized fungi in chronically contaminated environments. This observation has led to the use of fungi in radiobiology studies, with the goal of finding novel resistance mechanisms that could assist fields such as nuclear medicine and space biology. As photonic (x-ray and γ-ray) exposure is the most widely available method for irradiation, little work has been done examining how fungi (other than budding yeast) respond to irradiation by ionizing particles (e.g. protons), although particle irradiation may cause distinct cellular damage, and it is more relevant to environmental exposure profiles. Here, we expand on a previous study of the melanized yeast Exophiala dermatitidis responding to γ-radiation exposure by characterizing the phenotypic and transcriptomic response to irradiation by three different ionizing particles: protons, deuterons, and α-particles. No significant difference in survival was observed between these strains under any condition, suggesting that melanin does not impart protection to acute irradiation to these particles. The transcriptomic response during recovery to particle exposure was similar to that observed after γ-irradiation, with DNA repair and replication genes upregulated, and genes involved in translation and ribosomal biogenesis being heavily repressed, indicating an attenuation of cell growth. However, a comparison of global gene expression showed clear clustering into particle and γ-radiation groups. The response elicited by particle irradiation was more complex. Compared to the γ-associated response, particle irradiation resulted in greater changes in gene expression, a more diverse set of differentially expressed genes, and a significant induction of gene categories such as autophagy and protein catabolism. Additionally, individual particle responses were analyzed and compared, resulting in the discovery of unique expression signatures and individual genes for each particle type that could be used as radio-nuclide discrimination markers. The strong response we observed here at the gene expression level inprovides insights into the unique types of damage that particle irradiation causes to fungal cells, allowing for future dissection of radiation source-specific resistance mechanisms.

show abstract

Nothing Special in the Specialist? Draft Genome Sequence of Cryomyces antarcticus, the Most Extremophilic Fungus from Antarctica

Cited by 23 publications

References 28 publications

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungal evolution: major ecological adaptations and evolutionary transitions

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

The transcriptomic and phenotypic response of the melanized yeast Exophiala dermatitidis to ionizing particle exposure

Contact Info

Product

Resources

About