Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey DOI Creative Commons
Michael Brysch‐Herzberg, Guo‐Song Jia, Matthias Sipiczki

et al.

Yeast, Journal Year: 2023, Volume and Issue: 40(7), P. 237 - 253

Published: May 27, 2023

Abstract Two strains of fission yeast were isolated from honey. They differ the type strain Schizosaccharomyces octosporus by three substitutions in D1/D2 domain nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting a 99.5% identity. In internal transcribed spacer (ITS) region (consisting ITS1, 5.8S rDNA, and ITS2), S. 16 gaps 91 substitutions, which is equivalent to an identity 88.1%. Genome sequencing on one new revealed that average nucleotide (ANI) between its genome reference 90.43% there exist major rearrangements two genomes. Mating analysis are completely reproductively separated. A strong prezygotic barrier exists few mating products consist diploid hybrids do not form recombinant ascospores. strains, asci either zygotic, arising conjugation, or they develop without conjugation asexual cells (azygotic). Compared currently recognized species, spectrum nutrients assimilated restricted. Of 43 carbohydrates included physiological standard tests, only 7 assimilated. According results sequence analysis, trials, phenotypic characterization, species lindneri described accommodate (holotype: CBS 18203 T ex‐type: MUCL 58363; MycoBank no.: MB 847838).

Language: Английский

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference DOI Creative Commons
Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li

et al.

PLoS Biology, Journal Year: 2020, Volume and Issue: 18(12), P. e3001007 - e3001007

Published: Dec. 2, 2020

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying removing these prior However, a recent study reported that doing so worsen inference, underscoring the need alternative alignment strategies. Here, we introduce ClipKIT, an software that, rather than putatively phylogenetically uninformative sites, instead aims identify retain parsimony-informative known be informative. To test efficacy examined accuracy support phylogenies inferred 14 strategies, including those implemented across nearly 140,000 broad sampling evolutionary histories. Phylogenies ClipKIT-trimmed accurate, robust, time saving. Furthermore, ClipKIT consistently outperformed other methods diverse datasets, suggesting based on retaining provide robust framework trimming.

Language: Английский

Citations

437

A genome-scale phylogeny of the kingdom Fungi DOI Creative Commons
Yuanning Li, Jacob L. Steenwyk, Ying Chang

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 31(8), P. 1653 - 1665.e5

Published: Feb. 19, 2021

Language: Английский

Citations

263

Evolution of the human pathogenic lifestyle in fungi DOI Creative Commons
Antonis Rokas

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(5), P. 607 - 619

Published: May 4, 2022

Fungal pathogens cause more than a billion human infections every year, resulting in 1.6 million deaths annually. Understanding the natural history and evolutionary ecology of fungi is helping us understand how disease-relevant traits have repeatedly evolved. Different types mechanisms genetic variation contributed to evolution fungal pathogenicity specific differences distinguish from non-pathogens. Insights into traits, elements, ecological that contribute are crucial for developing strategies both predict emergence develop drugs combat them.

Language: Английский

Citations

160

PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data DOI
Jacob L. Steenwyk, Thomas J. Buida, Abigail L. LaBella

et al.

Bioinformatics, Journal Year: 2021, Volume and Issue: 37(16), P. 2325 - 2331

Published: Feb. 5, 2021

Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) phylogenetic trees to evaluate their information content, infer evolutionary events processes predict gene function. However, automated processing of MSAs remains a challenge due the lack unified toolkit. To fill this gap, we introduce PhyKIT, toolkit for UNIX shell environment with 30 functions that trees, including but not limited estimation mutation rate, evaluation composition biases, calculation degree violation molecular clock collapsing bipartitions (internal branches) low support.To demonstrate utility detail three use cases: (1) summarizing content diagnosing potential biases or tree data; (2) evaluating gene-gene covariation rates identify functional relationships, novel ones, among genes (3) resolution polytomies which are suggestive rapid radiation data. We anticipate PhyKIT will be useful processing, examining deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under MIT license extensive documentation user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data at Bioinformatics online.

Language: Английский

Citations

158

Integrative approaches for species delimitation in Ascomycota DOI
Sajeewa S. N. Maharachchikumbura, Yanpeng Chen, Hiran A. Ariyawansa

et al.

Fungal Diversity, Journal Year: 2021, Volume and Issue: 109(1), P. 155 - 179

Published: July 1, 2021

Language: Английский

Citations

134

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina DOI Creative Commons
Marizeth Groenewald, Chris Todd Hittinger,

Konstanze Bensch

et al.

Studies in Mycology, Journal Year: 2023, Volume and Issue: 105(1), P. 1 - 22

Published: May 26, 2023

Language: Английский

Citations

64

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts DOI
Dana A. Opulente, Abigail L. LaBella, Marie‐Claire Harrison

et al.

Science, Journal Year: 2024, Volume and Issue: 384(6694)

Published: April 25, 2024

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Two general paradigms have been proposed explain this variation: (i) trade-offs between performance efficiency and breadth (ii) the joint influence of extrinsic (environmental) intrinsic (genomic) factors. We assembled genomic, metabolic, data nearly all known species ancient fungal subphylum Saccharomycotina (1154 yeast strains 1051 species), grown 24 different environmental conditions, examine evolution. found that large differences carbon utilization traits yeasts stem genes encoding specific metabolic pathways, but we limited evidence for trade-offs. These comprehensive argue factors shape microbes.

Language: Английский

Citations

42

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes DOI Creative Commons
Emile Gluck‐Thaler,

Timothy I. Ralston,

Zachary Konkel

et al.

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(5)

Published: May 1, 2022

Accessory genes are variably present among members of a species and reservoir adaptive functions. In bacteria, differences in gene distributions individuals largely result from mobile elements that acquire disperse accessory as cargo. contrast, the impact cargo-carrying on eukaryotic evolution remains unknown. Here, we show variation genome content within multiple fungal is facilitated by Starships, newly discovered group massive 110 kb long average, share conserved components, carry diverse arrays genes. We identified hundreds Starship-like regions across every major class filamentous Ascomycetes, including 28 distinct Starships range 27 to 393 last shared common ancestor ca. 400 Ma. Using new long-read assemblies plant pathogen Macrophomina phaseolina, characterize four additional whose activities contribute standing structure content. One these elements, Voyager, inserts into 5S rDNA contains candidate virulence factor increasing copy number has contrasting associations with pathogenic saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. propose analogs bacterial integrative conjugative based parallels between their components may therefore represent first dedicated agents active transfer eukaryotes. Our results suggest have shaped genomes for millions years reveal concerted route throughout entire phylum.

Language: Английский

Citations

71

Classes and phyla of the kingdom Fungi DOI Creative Commons
Nalin N. Wijayawardene, Kevin D. Hyde, Kirill V. Mikhailov

et al.

Fungal Diversity, Journal Year: 2024, Volume and Issue: 128(1), P. 1 - 165

Published: Oct. 15, 2024

Abstract Fungi are one of the most diverse groups organisms with an estimated number species in range 2–3 million. The higher-level ranking fungi has been discussed framework molecular phylogenetics since Hibbett et al., and definition higher ranks (e.g., phyla) ‘true fungi’ have revised several subsequent publications. Rapid accumulation novel genomic data advancements now facilitate a robust precise foundation for classification within kingdom. This study provides updated kingdom , drawing upon comprehensive phylogenomic analysis Holomycota which we outline well-supported nodes fungal tree explore more contentious groupings. We accept 19 phyla Fungi, viz . Aphelidiomycota Ascomycota Basidiobolomycota Basidiomycota Blastocladiomycota Calcarisporiellomycota Chytridiomycota Entomophthoromycota Entorrhizomycota Glomeromycota Kickxellomycota Monoblepharomycota Mortierellomycota Mucoromycota Neocallimastigomycota Olpidiomycota Rozellomycota Sanchytriomycota, Zoopagomycota In phylogenies, Caulochytriomycota resides ; thus, former is regarded as synonym latter, while Caulochytriomycetes viewed class provide description each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov introduced only subphylum Sanchytriomycota subclass Pneumocystomycetidae Kirk al. Pneumocystomycetes invalid thus validated. Placements fossil classes also discussed, providing examples.

Language: Английский

Citations

11

Exploiting synthetic biology platforms for enhanced biosynthesis of natural products in Yarrowia lipolytica DOI

Dahai Jiang,

Manqi Yang,

Kai Chen

et al.

Bioresource Technology, Journal Year: 2024, Volume and Issue: 399, P. 130614 - 130614

Published: March 19, 2024

Language: Английский

Citations

10