Genome-wide patterns of noncoding and protein-coding sequence variation in the major fungal pathogen Aspergillus fumigatus DOI Creative Commons
Alec Brown, Jacob L. Steenwyk, Antonis Rokas

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(7)

Published: May 2, 2024

Abstract Aspergillus fumigatus is a deadly fungal pathogen, responsible for >400,000 infections/year and high mortality rates. A. strains exhibit variation in infection-relevant traits, including their virulence. However, most protein-coding genes, those that modulate its virulence, are shared between closely related nonpathogenic relatives. We hypothesized genes substantial genetic the noncoding regions immediately upstream to start codons of which could reflect differences gene regulation strains. To begin testing this hypothesis, we identified 5,812 single-copy orthologs across genomes 263 In general, showed higher levels sequence compared with corresponding regions. Focusing on 2,482 whose identity scores ranged 75 99%, 478 total signatures positive selection only 65 Twenty-eight 5 under associated known Noncoding region included single-nucleotide polymorphisms insertions or deletions at least few nucleotides. These results show harbor greater than regions, raising hypothesis may contribute phenotypic heterogeneity.

Language: Английский

OMICS and Other Advanced Technologies in Mycological Applications DOI Creative Commons
Nalin N. Wijayawardene, Nattawut Boonyuen, C. B. Ranaweera

et al.

Journal of Fungi, Journal Year: 2023, Volume and Issue: 9(6), P. 688 - 688

Published: June 19, 2023

Fungi play many roles in different ecosystems. The precise identification of fungi is important aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate taxonomy, higher-level classifications. However, some species, referred to "dark taxa", lack distinct physical features that makes their challenging. High-throughput metagenomics environmental samples provide a solution identifying new lineages fungi. This paper discusses approaches including PCR amplification rDNA, multi-loci phylogenetic analyses, the importance various omics (large-scale molecular) techniques for understanding fungal applications. use proteomics, transcriptomics, metatranscriptomics, metabolomics, interactomics provides comprehensive These advanced technologies are critical expanding knowledge Kingdom Fungi, its impact food safety security, edible mushrooms foodomics, secondary metabolites, mycotoxin-producing fungi, biomedical therapeutic applications, antifungal drugs drug resistance, data novel development. also highlights exploring from extreme environments understudied areas identify dark taxa.

Language: Английский

Citations

31
Statistical optimization of pectinases from thermophilic Aspergillus fumigatus BT-4 employing response surface methodology through submerged fermentation using agricultural wastes DOI Creative Commons
Imran Ali, Roheena Abdullah,

Sana Ullah Saqib

et al.

BMC Biotechnology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 4, 2025

In this study, thermophilic pectinase-producing strains were isolated. Among all the isolates, strain No. 4 was identified as Aspergillus fumigatus BT-4 based on its morphology and 18 S rDNA analysis. This employed to screen various fermentation media enhance pectinase production. Pectinases are crucial enzymes with significant industrial applications, particularly in food textile industries. Identifying efficient producers optimizing their production processes essential for improving applications. Maximum observed using 1% grapefruit peel M5 media. Shake flask kinetics demonstrated highest values of specific rate constant (qp), growth (µ), product yield coefficient (Yp/x), volumetric formation (Qp), biomass (Qx) after 72 h incubation. Furthermore, Optimization components via Response Surface Methodology (RSM) improved by 50%, showcasing effectiveness factorial central composite designs fine-tuning parameters. The use agricultural waste (grapefruit peel) significantly reduced costs, offering an economically viable substrate alternative. enzyme purified through ammonium sulfate precipitation, gel filtration, ion-exchange chromatography, resulting a 2.3-fold purification. molecular weight determined be 48 kDa. Enzyme kinetics, Lineweaver-Burk plot at pectin concentrations, showed Vmax 32.7 UmL− 1 Km 0.3 mg mL− 1. Thermodynamic parameters, including activation energy (Ea), enthalpy (ΔH), entropy (ΔS), measured 41.74 kJmol− 1, 39.53 46.9 respectively. study successfully isolated potent producer. process enhanced Using reduces costs eliminating need expensive raw materials utilizing low-cost, sustainable, locally available substrate. approach also minimizes disposal expenses, making more economical. effectively purified, kinetic thermodynamic properties thoroughly characterized, revealing potential comprehensive analysis optimization strategies provides robust foundation scaling up production, contributing cost-effective processes.

Language: Английский

Citations

1
Reducing the number of accepted species inAspergillusseriesNigri DOI Creative Commons
Chao Bian, Yoko Kusuya, F. Sklenář

et al.

Studies in Mycology, Journal Year: 2022, Volume and Issue: 102(1), P. 95 - 132

Published: June 30, 2022

Language: Английский

Citations

29
Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond DOI Creative Commons
Jacob L. Steenwyk, Antonis Rokas, Gustavo H. Goldman

et al.

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(10), P. e1011704 - e1011704

Published: Oct. 19, 2023

If you know the enemy and yourself, need not fear result of a hundred battles.If yourself but enemy, for every victory gained will also suffer defeat.If neither nor succumb in battle."-SunTzu, The Art War Fungal pathogens threaten human welfare, including animal health global food security.For example, ameliorating crop loss due to fungal plant would feed nearly 600 million more people [1].Fungal infections humans are difficult diagnose treat, potentially leading serious illness death, especially immunocompromised individuals; case point, there an estimated 1.7 deaths per year than 150 severe worldwide [2].These issues may be exacerbated climate change.Reflecting importance combatting preventing infection diseases caused by fungi, World Health Organization recently released list priority (https://www.who.int/publications/i/item/9789240060241).Accordingly, fungi that cause disease have become major research focus, resulting deeper, still incomplete, understanding virulence cadre pathogenic species.Most opportunistic affect individuals.This suggests any fungus capable growing body overcoming or evading compromised immune system could disease.Supporting this notion, advances DNA sequencing clinical isolates led realization cryptic speciesmorphologically indistinguishable from known genetically distinct-are underappreciated source [3][4][5][6].Cryptic species been identified several genera agricultural biomedical significance, such as (e.g., Fusarium) [7] Aspergillus; Table 1) [3].Due morphological similarities (Fig 1 ), using typical microbiology techniques setting, incomplete their epidemiology burden.Here, avenues aim enrich our pathogens-as well other pathogens-and diminish impact on welfare discussed.Cryptic genus Aspergillus used example.We argue infections, among which little is known, can reduced if we in-depth pathogens, humans, interaction between two.

Language: Английский

Citations

11
PhyKIT: A Multitool for Phylogenomics DOI Creative Commons
Jacob L. Steenwyk, Gemma I. Martínez‐Redondo, Thomas J. Buida

et al.

Current Protocols, Journal Year: 2024, Volume and Issue: 4(11)

Published: Oct. 30, 2024

Abstract Multiple sequence alignments and phylogenetic trees are rich in biological information fundamental to research biology. PhyKIT is a tool for processing analyzing the content of multiple trees. Here, we describe how use diverse analyses, including (i) constructing phylogenomic supermatrix, (ii) detecting errors orthology inference, (iii) quantifying biases data sets, (iv) identifying radiation events or lack resolution using gene support frequencies, (v) conducting evolution‐based screens facilitate function prediction. Several functions that streamline alignment processing—such as renaming FASTA entries tree tips—are also discussed. These protocols demonstrate simple command‐line operations unified framework analysis processing, from supermatrix construction diagnosis gaining clues about function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Installing syntax usage 2 Constructing 3 Detecting anomalies relationships 4 Quantifying matrices related measures 5 Identifying polytomies 6 Assessing gene‐gene coevolution genetic screen

Language: Английский

Citations

2
The relevance of genomics in food mycology with a focus on food safety DOI
Jéssica Gil-Serna, Covadonga Vázquez, Belén Patiño

et al.

Current Opinion in Food Science, Journal Year: 2024, Volume and Issue: 59, P. 101213 - 101213

Published: Aug. 23, 2024

Language: Английский

Citations

1
Strain heterogeneity in a non-pathogenic Aspergillus fungus highlights factors associated with virulence DOI Creative Commons
David C. Rinker, Thomas J. C. Sauters, Karin Steffen

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Sept. 4, 2024

Language: Английский

Citations

1
Reticulate evolution: Detection and utility in the phylogenomics era DOI Creative Commons

Saelin Bjornson,

Heroen Verbruggen, Nathan S. Upham

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 201, P. 108197 - 108197

Published: Sept. 11, 2024

Language: Английский

Citations

1
Genome-wide patterns of non-coding sequence variation in the major fungal pathogenAspergillus fumigatus DOI Creative Commons
Alec Brown, Jacob L. Steenwyk, Antonis Rokas

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 9, 2024

Abstract A. fumigatus is a deadly fungal pathogen, responsible for >400,000 infections/year and high mortality rates. strains exhibit variation in infection-relevant traits, including their virulence. However, most protein-coding genes, those that modulate its virulence, are shared between closely related non-pathogenic relatives. We hypothesized genes substantial genetic the non-coding regions immediately upstream to start codons of which could reflect differences gene regulation strains. To begin testing this hypothesis, we identified 5,812 single-copy orthologs across genomes 263 showed higher levels sequence compared corresponding regions. Specifically, found 1,274 exhibited <75% nucleotide similarity (compared 928 regions) 3,721 75% 99% 2,482 Only 817 ≥99% 2,402 By examining whose identity scores ranged 99%, 478 total with signatures positive selection only 65 28 5 under associated known Non-coding region included single polymorphisms insertions or deletions at least few nucleotides. These results show harbor greater than regions, raising hypothesis may contribute phenotypic heterogeneity.

Language: Английский

Citations

0
Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence DOI Creative Commons
David C. Rinker, Thomas J. C. Sauters, Karin Steffen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 10, 2024

Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., ability to cause morbidity and mortality) of 16 diverse strains

Language: Английский

Citations

0