ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

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

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A genome-scale phylogeny of the kingdom Fungi

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

Published: Feb. 19, 2021

Language: Английский

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Evolution of the human pathogenic lifestyle in fungi

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

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PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data

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

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Integrative approaches for species delimitation in Ascomycota

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

Published: July 1, 2021

Language: Английский

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A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

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

Published: May 26, 2023

Language: Английский

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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

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

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Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

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

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Classes and phyla of the kingdom Fungi

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

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

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

Published: March 19, 2024

Language: Английский

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