Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Batista, Thiago Mafra; Hilário, Heron O.; Brito, Gabriel Antônio Mendes de; Moreira, Rennan Garcias; Furtado, Carolina; Menezes, Graciéle Cunha Alves de; Rosa, Carlos A.; Rosa, Luiz Henrique; Franco, Glória Regina

doi:10.1016/j.ygeno.2020.05.004

Cited by 21 publications

(17 citation statements)

References 44 publications

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“…A putative IBP of 236 amino acids that shared sequence similarities with two IBP isoforms from the closely related A. psychrotrophicus was identified. Such discovery confirmed these two Antarctomyces species the only ascomycetous fungi able to produce AFP [89].…”

Section: Extremophilic/polyextremotolerant Fungisupporting

confidence: 68%

“…A few years ago, a novel psychrophilic, endemic fungus was described for Antarctica, Antarctomyces pellizariae (Thelebolales, Leotiomycetes, Ascomycota; [89]). Recently, both its nuclear and mitochondrial genomes were mined in search of secondary metabolite gene clusters and genes coding for AFP and IBP proteins [89]. Within the mitochondrial genome the gene arrangement was found in line with that of other 16 Leotiomycetes and four Pseudogymnoascus species.…”

Section: Extremophilic/polyextremotolerant Fungimentioning

confidence: 99%

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An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia

Ametrano

Sterflinger

et al. 2020

Life

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Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

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Section: Extremophilic/polyextremotolerant Fungisupporting

confidence: 68%

Section: Extremophilic/polyextremotolerant Fungimentioning

confidence: 99%

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia

Ametrano

Sterflinger

et al. 2020

Life

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“…MAPK cascades, and calcium-dependent protein kinase were identified to regulate cold stress through modulating ICE1 protein stability in plants [ 7 , 8 ]. Secondary metabolites play important roles during cold stress in plants and fungi [ 9 , 10 ]. Four down-regulated transcripts were encoded by VVO_00003, VVO_00004, VVO_00010, and VVO_00030, respectively.…”

Section: Resultsmentioning

confidence: 99%

The cold - resistance mechanism of a mutagenic Volvariella volvacea strain VH3 with outstanding traits revealed by transcriptome profiling

Liu

et al. 2021

BMC Microbiol

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Background The straw mushroom (Volvariella volvacea) is one of the important vegetables that is popular for its delicious taste. However, the straw mushroom is sensitive to low temperature, resulting in economic loss during transportation and storage. We obtained a novel straw mushroom strain, named VH3, via ultraviolet mutagenesis. Results Our study revealed that VH3 exhibited high cold resistance compared to an ordinary straw mushroom cultivar, V23. We found that the electrolyte leakages of VH3 were always significantly lower than that of V23 treated with 4 °C for 0 h, 2 h,4 h, 8 h, 16 h, and 24 h. Before cold treatment (0 h), there were no difference of MDA contents, SOD activities, and CAT activities between VH3 and V23. At the late stage (8 h, 26 h, and 24 h) of cold treatment, the MDA contents of VH3 were lower while both the SOD and CAT activities were higher than those of V23. To investigate the potential mechanisms of VH3 cold resistance, we performed transcriptome sequencing to detect the transcriptome profiling of VH3 and V23 after 0 h and 4 h cold treatment. Transcriptome sequencing revealed that 111 differentially expressed genes (DEG) between V23 (0 h) and VH3 (0 h) (V23–0_vs_VH3–0), consisting 50 up-regulated and 61 down-regulated DEGs. A total of 117 DEGs were obtained between V23 (4 h) and VH3(4 h) (V23–4_vs_VH3–4), containing 94 up-regulated and 23 down-regulated DEGs. Among these DEGs, VVO_00021 and VVO_00017 were up-regulated while VVO_00003, VVO_00004, VVO_00010, and VVO_00030 were down-regulated in V23–0_vs_VH3–0 and VH3–4_vs_V23–4. KEGG and GO analysis revealed that the 6 DEGs were annotated to pathways related to cold stress. Besides, the GA3 content was also decreased in VH3. Conclusions Collectively, our study first revealed that the increased cold resistance of VH3 might be caused by the expression change of VVO_00003, VVO_00004, VVO_00017, VVO_00021, and VVO_00030, and decreased GA3.

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“…Species of Thelebolus have cleistothecioid ascomata with variable numbers of ascospores per ascus, ranging from 8 to more than 1000 spores (Kimbrough, 1981a). An expansive definition of the order now includes Pseudeurotiaceae in addition to Thelebolaceae Batista et al, 2020). Coprophilic and psychrophilic species are found in both of these families (Robinson, 2001;de Hoog et al, 2005) although morphologically they differ significantly, hence their previously unrecognized relationship (Baral, 2016).…”

Section: Thelebolalesmentioning

confidence: 99%