scholarly journals Fungal evolution: cellular, genomic and metabolic complexity

2020 ◽  
Author(s):  
Miguel A. Naranjo‐Ortiz ◽  
Toni Gabaldón
Keyword(s):  
Fungal Evolution

An Optimized Method for the Preparation of Monascus purpureus DNA for Genome Sequencing

2014 ◽  
Vol 563 ◽  
pp. 379-383 ◽  
Author(s):  
Yue Yang ◽  
Xin Jun Du ◽  
Ping Li ◽  
Bin Liang ◽  
Shuo Wang
Keyword(s):  
Genome Sequencing ◽  
Genomic Dna ◽  
Benzyl Chloride ◽  
Monascus Purpureus ◽  
Sequencing Technologies ◽  
Fungal Evolution ◽  
Ctab Method ◽  
Fungal Dna ◽  
Gene Functional Analysis ◽  
Generation Sequencing

More and more attention has been paid to filamentous fungal evolution, metabolic pathway and gene functional analysis via genome sequencing. However, the published methods for the extraction of fungal genomic DNA were usually costly or inefficient. In the present study, we compared five different DNA extraction protocols: CTAB protocol with some modifications, benzyl chloride protocol with some modifications, snailase protocol, SDS protocol and extraction with the E.Z.N.A. Fungal DNA Maxi Kit (Omega Bio-Tek, USA). The CTAB method which we established with some modification in several steps is not only economical and convenient, but also can be reliably used to obtain large amounts of highly pure genomic DNA fromMonascus purpureusfor sequencing with next-generation sequencing technologies (Illumina and 454) successfully.

scholarly journals Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

2019 ◽  
Vol 94 (6) ◽  
pp. 2101-2137 ◽  
Author(s):  
Miguel A. Naranjo‐Ortiz ◽  
Toni Gabaldón
Keyword(s):  
Fungal Evolution

Phosphorylation and fungal evolution

Science ◽  
2016 ◽  
Vol 354 (6309) ◽  
pp. 192-193
Author(s):  
L. M. Zahn
Keyword(s):  
Fungal Evolution

scholarly journals Chytrid rhizoid morphogenesis is adaptive and resembles hyphal development in ‘higher’ fungi

2019 ◽  
Author(s):  
Davis Laundon ◽  
Nathan Chrismas ◽  
Glen Wheeler ◽  
Michael Cunliffe
Keyword(s):  
Cell Biology ◽  
Developmental Plasticity ◽  
Common Ancestor ◽  
Spatial Differentiation ◽  
Morphological Plasticity ◽  
Recent Common Ancestor ◽  
Significant Component ◽  
Most Recent Common Ancestor ◽  
Fungal Evolution ◽  
Dependent Cell

AbstractFungi are major components of the Earth’s biosphere [1], sustaining many critical ecosystem processes [2, 3]. Key to fungal prominence is their characteristic cell biology, our understanding of which has been principally based on ‘higher’ dikaryan hyphal and yeast forms [4–6]. The early-diverging Chytridiomycota (chytrids) are ecologically important [2, 7, 8] and a significant component of fungal diversity [9–11], yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids [12]. The evolution of fungal hyphae appears to have occurred from lineages exhibiting rhizoidal growth [13] and it has been hypothesised that a rhizoid-like structure was the precursor to multicellular hyphae and mycelial feeding in fungi [14]. Here we show in a unicellular chytrid, Rhizoclosmatium globosum, that rhizoid development has equivalent features to dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous properties with growth in hyphal forms, including tip production, branching and decreasing fractal geometry towards the growing edge, and is controlled by β-glucan-dependent cell wall synthesis and actin polymerisation. Chytrid rhizoids from individual cells also demonstrate adaptive morphological plasticity in response to substrate availability, developing a searching phenotype when carbon starved and exhibiting spatial differentiation when interacting with particulate substrates. Our results show striking similarities between unicellular early-diverging and dikaryan fungi, providing insights into chytrid cell biology, ecological prevalence and fungal evolution. We demonstrate that the sophisticated cell biology and developmental plasticity previously considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.

scholarly journals Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

2021 ◽  
Author(s):  
Francesco Dal Grande ◽  
Veronique Jamilloux ◽  
Nathalie Choisne ◽  
Anjuli Calchera ◽  
Malte Petersen ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Phenotypic Diversity ◽  
Elevation Gradients ◽  
Climate Niche ◽  
Fungal Evolution ◽  
Specific Distribution ◽  
Fungal Adaptation ◽  
The Impact ◽  
Insertion Frequency

Background: Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. Results: We found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. Conclusions: This pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.

scholarly journals Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

2021 ◽  
Author(s):  
Giselle C. Martin-Hernandez ◽  
Bettina Müller ◽  
Christian Brandt ◽  
Martin Hölzer ◽  
Adrian Viehweger ◽  
...  
Keyword(s):  
Gc Content ◽  
Pairwise Identity ◽  
Protein Coding ◽  
Intraspecific Divergence ◽  
Protein Coding Genes ◽  
Fungal Evolution ◽  
Lignocellulose Hydrolysate ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

scholarly journals Fungal Evolution: Mucor and Phycomyces See Double

2016 ◽  
Vol 26 (16) ◽  
pp. R775-R777 ◽  
Author(s):  
Jason E. Stajich
Keyword(s):  
Fungal Evolution

Fungal Evolution Meets Fungal Genomics

2003 ◽  
Author(s):  
Jessica Leigh ◽  
Elias Seif ◽  
Naiara Rodriguez-Ezpeleta ◽  
Yannick Jacob ◽  
B Franz Lang
Keyword(s):  
Fungal Genomics ◽  
Fungal Evolution

scholarly journals A multigene phylogeny of Olpidium and its implications for early fungal evolution

2011 ◽  
Vol 11 (1) ◽  
pp. 331 ◽  
Author(s):  
Satoshi Sekimoto ◽  
D'Ann Rochon ◽  
Jennifer E Long ◽  
Jaclyn M Dee ◽  
Mary L Berbee
Keyword(s):  
Multigene Phylogeny ◽  
Fungal Evolution
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