Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
- Klíčová slova
- Arctic biology, TE proliferation, biotrophy–saprotrophy evolution, carbon degradation, fungal genomics, fungal guild, genome size diversity, plant-fungus interactions, root-associations, saprotrophs,
- MeSH
- Agaricales * genetika MeSH
- fylogeneze MeSH
- genom fungální * genetika MeSH
- molekulární evoluce MeSH
- přenos genů horizontální MeSH
- rostliny mikrobiologie genetika MeSH
- transpozibilní elementy DNA genetika MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- transpozibilní elementy DNA MeSH
Candida krusei is a pathogenic yeast species that is phylogenetically outside both of the well-studied yeast groups, whole genome duplication and CUG. Like all other yeast species, it needs to accumulate high amounts of potassium cations, which are needed for proliferation and many other cell functions. A search in the sequenced genomes of nine C. krusei strains revealed the existence of two highly conserved genes encoding putative potassium uptake systems. Both of them belong to the TRK family, whose members have been found in all the sequenced genomes of species from the Saccharomycetales subclade. Analysis and comparison of the two C. krusei Trk sequences revealed all the typical features of yeast Trk proteins but also an unusual extension of the CkTrk2 hydrophilic N-terminus. The expression of both putative CkTRK genes in Saccharomyces cerevisiae lacking its own potassium importers showed that only CkTrk1 is able to complement the absence of S. cerevisiae's own transporters and provide cells with a sufficient amount of potassium. Interestingly, a portion of the CkTrk1 molecules were localized to the vacuolar membrane. The presence of CkTrk2 had no evident phenotype, due to the fact that this protein was not correctly targeted to the S. cerevisiae plasma membrane. Thus, CkTrk2 is the first studied yeast Trk protein to date that was not properly recognized and targeted to the plasma membrane upon heterologous expression in S. cerevisiae.
- Klíčová slova
- Candida, Trk proteins, cation homeostasis, potassium uptake, yeast K+ transporters,
- MeSH
- Candida klasifikace genetika růst a vývoj metabolismus MeSH
- draslík metabolismus MeSH
- fungální proteiny genetika metabolismus MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom fungální genetika MeSH
- iontový transport MeSH
- proteiny přenášející kationty genetika metabolismus MeSH
- rekombinantní proteiny genetika metabolismus MeSH
- Saccharomyces cerevisiae klasifikace genetika růst a vývoj metabolismus MeSH
- Saccharomycetales klasifikace genetika MeSH
- testy genetické komplementace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- draslík MeSH
- fungální proteiny MeSH
- proteiny přenášející kationty MeSH
- rekombinantní proteiny MeSH
Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.
We report an optimized low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable with those of regular, higher input amounts, and allow the use of 100-fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility of studying colony cell subpopulations, or those that can be isolated directly from environmental samples.
- Klíčová slova
- HTS, NGS, Saccharomyces cerevisiae, chromatin-accessibility, epigenetics,
- MeSH
- chromatin chemie genetika metabolismus MeSH
- formaldehyd chemie MeSH
- genom fungální genetika MeSH
- počet buněk MeSH
- regulační oblasti nukleových kyselin MeSH
- reprodukovatelnost výsledků MeSH
- Saccharomyces cerevisiae genetika MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- chromatin MeSH
- formaldehyd MeSH
Protoplasts were isolated from two isolates each of Beauveria bassiana and Metarhizium anisopliae using lysing enzymes. Intra- and intergeneric protoplast fusion has been carried out using 40% polyethylene glycol. The fused protoplasts of B. bassiana and M. anisopliae have been regenerated on Czapek-Dox agar media, and a total of four fusants were selected for further studies. An increase in proteinase and chitinase enzyme activity was recorded with all fusants as compared to the wild-type isolates. To understand the nature of recombination process, random amplification of polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) were carried out on genomic DNA of fused and wild-type isolates. The present study demonstrates the scope and significance of the protoplast fusion technique as a rapid consistent method for identification of B. bassiana and M. anisopliae fused and wild-type isolates based on the banding pattern of RAPD and RFLP that can be reliably used ahead for further applications on these species.
- MeSH
- Beauveria genetika metabolismus MeSH
- chitinasy metabolismus MeSH
- genom fungální genetika MeSH
- Metarhizium genetika metabolismus MeSH
- polymorfismus genetický MeSH
- proteasy metabolismus MeSH
- protoplasty metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- chitinasy MeSH
- proteasy MeSH
The Agrobacterium tumefaciens-mediated transformation of the zygomycetous fungus Mucor circinelloides is described. A method was also developed for the hygromycin B-based selection of Mucor transformants. Transformation with the hygromycin B phosphotransferase gene of Escherichia coli controlled by the heterologous Aspergillus nidulans trpC promoter resulted in hygromycin B-resistant clones. The presence of the hygromycin resistance gene in the genome of the transformants was verified by polymerase chain reaction and Southern hybridization: the latter analyses revealed integrations in the host genome at different sites in different transformants. The stability of transformants remained questionable during the latter analyses.
- MeSH
- Agrobacterium tumefaciens genetika MeSH
- antifungální látky farmakologie MeSH
- Aspergillus nidulans genetika MeSH
- DNA fungální analýza genetika MeSH
- Escherichia coli enzymologie genetika MeSH
- exprese genu MeSH
- fosfotransferasy s alkoholovou skupinou jako akceptorem genetika MeSH
- fungální léková rezistence genetika MeSH
- genom fungální genetika MeSH
- geny hub MeSH
- hygromycin B farmakologie MeSH
- klonování DNA MeSH
- Mucor genetika MeSH
- polymerázová řetězová reakce MeSH
- promotorové oblasti (genetika) MeSH
- proteiny z Escherichia coli genetika MeSH
- rekombinantní proteiny metabolismus MeSH
- selekce (genetika) MeSH
- Southernův blotting MeSH
- transformace genetická * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- antifungální látky MeSH
- DNA fungální MeSH
- fosfotransferasy s alkoholovou skupinou jako akceptorem MeSH
- hygromycin B MeSH
- hygromycin-B kinase MeSH Prohlížeč
- proteiny z Escherichia coli MeSH
- rekombinantní proteiny MeSH
