4.6 Article

The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events

Lotus A. Lofgren et al.

Summary: Birds are highly susceptible to aspergillosis, however, the pathogenicity factors associated with aspergillosis in wild birds have not been examined. This study found that avian aspergillosis is not contagious among wild birds and is likely driven by environmental factors or host comorbidities.

G3-GENES GENOMES GENETICS (2022)

Article Computer Science, Artificial Intelligence

Empirical evaluation of methods for de novo genome assembly

Firaol Dida et al.

Summary: This article explores the rapid growth of high-throughput sequencing projects and new read-assembly algorithms driven by next-generation sequencing technologies like Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for various organisms, with de novo assembly playing a crucial role in gene discovery and other studies. The article provides a thorough comparison of different assembly algorithms to aid new users in understanding them better.

PEERJ COMPUTER SCIENCE (2021)

Article Biochemistry & Molecular Biology

Dsuite - Fast D-statistics and related admixture evidence from VCF files

Milan Malinsky et al.

Summary: Dsuite is an efficient software package that allows genome scale calculations of the D and f(4)-ratio statistics from VCF files, enabling evaluation of all combinations of multiple populations or species, particularly suited for larger genomic data sets.

MOLECULAR ECOLOGY RESOURCES (2021)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

Amelia E. Barber et al.

Summary: The study identified the pan-genome of Aspergillus fumigatus using 300 globally sampled genomes, with findings showing the presence of core genes in all isolates alongside variability in 16-22% of the genome. Clinical isolates were found to be enriched in a genetic cluster with more accessory genes related to transporters, iron-binding activity, and metabolism. Genome-wide association studies revealed genetic variation associated with human infection and drug resistance, providing insight into potential therapeutic targets.

NATURE MICROBIOLOGY (2021)

Article Evolutionary Biology

The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades

Markus Hiltunen et al.

Summary: Marasmius oreades, commonly known as the Scotch bonnet or fairy-ring mushroom, has a nearly gapless chromosome and mitochondrion sequences presented in this study, along with high-quality gene annotation and repeat library. These data resources provide an opportunity to answer detailed questions about mushroom evolution, as genome assemblies of mushroom-forming fungi with complete chromosome sequences are currently rare.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Microbiology

Aspergillus fumigatus In-Host HOG Pathway Mutation for Cystic Fibrosis Lung Microenvironment Persistence

Brandon S. Ross et al.

Summary: This study collected A. fumigatus isolates from a CF patient over 4.5 years, revealing both transient and persistent strains. Persistent isolates harbored a unique adaptive genotype, laying the foundation for identifying persistent isolates that may require antifungal therapy.
Article Biochemical Research Methods

OptM: estimating the optimal number of migration edges on population trees using Treemix

Robert R. Fitak

Summary: The study shows that inferring the optimal number of migration events in population trees can be achieved by examining the second-order rate of change in likelihood (Δm), which performs equally well as current recommendations for Treemix. This method may be preferable in large, complex population histories.

BIOLOGY METHODS & PROTOCOLS (2021)

Article Biochemistry & Molecular Biology

A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

Nathan A. Wyatt et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2020)

Review Mycology

Exploring the molecular mechanism of azole resistance in Aspergillus fumigatus

P. Chen et al.

JOURNAL DE MYCOLOGIE MEDICALE (2020)

Article Biology

Fungal evolution: cellular, genomic and metabolic complexity

Miguel A. Naranjo-Ortiz et al.

BIOLOGICAL REVIEWS (2020)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Budding yeast complete DNA synthesis after chromosome segregation begins

Tsvetomira Ivanova et al.

NATURE COMMUNICATIONS (2020)

Article Microbiology

On Variant Discovery in Genomes of Fungal Plant Pathogens

Lizel Potgieter et al.

FRONTIERS IN MICROBIOLOGY (2020)

Review Plant Sciences

The rise and fall of genes: origins and functions of plant pathogen pangenomes

Thomas Badet et al.

CURRENT OPINION IN PLANT BIOLOGY (2020)

Article Respiratory System

Parasexual recombination enables Aspergillus fumigatus to persist in cystic fibrosis

Tobias Engel et al.

ERJ OPEN RESEARCH (2020)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Microbiology

Fungal biofilm morphology impacts hypoxia fitness and disease progression

Caitlin H. Kowalski et al.

NATURE MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

UniProt: a worldwide hub of protein knowledge

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Immunology

Aerosol Transmission of Aspergillus fumigatus in Cystic Fibrosis Patients in the Netherlands

Tobias G. P. Engel et al.

EMERGING INFECTIOUS DISEASES (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse

Paula Fagundes de Gouvea et al.

BMC GENOMICS (2018)

Article Genetics & Heredity

In-host microevolution of Aspergillus fumigatus: A phenotypic and genotypic analysis

Eloise Ballard et al.

FUNGAL GENETICS AND BIOLOGY (2018)

Article Biochemistry & Molecular Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Genetics & Heredity

Inferring Variation in Copy Number Using High Throughput Sequencing Data in R

Brian J. Knaus et al.

FRONTIERS IN GENETICS (2018)

Article Microbiology

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Evelina Y. Basenko et al.

JOURNAL OF FUNGI (2018)

Article Immunology

Hospitalized Patient as Source of Aspergillus fumigatus, 2015

Baptiste Lemaire et al.

EMERGING INFECTIOUS DISEASES (2018)

Article Biochemistry & Molecular Biology

VCFR: a package to manipulate and visualize variant call format data in R

Brian J. Knaus et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biochemistry & Molecular Biology

InterPro in 2017-beyond protein family and domain annotations

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Genetics & Heredity

A Unified Characterization of Population Structure and Relatedness

Bruce S. Weir et al.

GENETICS (2017)

Article Biochemistry & Molecular Biology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Editorial Material Microbiology

Heterogeneity Confounds Establishment of a Model Microbial Strain

Nancy P. Keller

Article Genetics & Heredity

A Unified Characterization of Population Structure and Relatedness

Bruce S. Weir et al.

GENETICS (2017)

Article Microbiology

Why prokaryotes have pangenomes

James O. McInerney et al.

NATURE MICROBIOLOGY (2017)

Article Biochemical Research Methods

GenomeScope: fast reference-free genome profiling from short reads

Gregory W. Vurture et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Heng Li

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Luigi Faino et al.

GENOME RESEARCH (2016)

Article Biology

Secondary metabolite arsenal of an opportunistic pathogenic fungus

Elaine Bignell et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)

Article Microbiology

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease

Jeffrey M. Flynn et al.

PLOS PATHOGENS (2016)

Review Microbiology

Epidemiological and Genomic Landscape of Azole Resistance Mechanisms in Aspergillus Fungi

Daisuke Hagiwara et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

Alison C. Testa et al.

BMC GENOMICS (2015)

Article Biochemistry & Molecular Biology

Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus

Natalie C. Bamford et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2015)

Article Genetics & Heredity

Repbase Update, a database of repetitive elements in eukaryotic genomes

Weidong Bao et al.

MOBILE DNA (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Biotechnology & Applied Microbiology

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Zhongtao Zhao et al.

BMC GENOMICS (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Microbiology

Aspergillus fumigatus-What Makes the Species a Ubiquitous Human Fungal Pathogen?

Kyung J. Kwon-Chung et al.

PLOS PATHOGENS (2013)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Genetics & Heredity

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

Joseph K. Pickrell et al.

PLOS GENETICS (2012)

Article Microbiology

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

Daniel Croll et al.

PLOS PATHOGENS (2012)

Article Biochemical Research Methods

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Ryan K. Dale et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

Chris A. Brown et al.

CURRENT BIOLOGY (2010)

Article Infectious Diseases

Azole antifungal resistance in Aspergillus fumigatus: 2008 and 2009

Ahmed Bueid et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Review Microbiology

Pathogenesis of Aspergillus fumigatus in Invasive Aspergillosis

Taylor R. T. Dagenais et al.

CLINICAL MICROBIOLOGY REVIEWS (2009)

Article Multidisciplinary Sciences

Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus

Celine M. O'Gorman et al.

NATURE (2009)

Article Infectious Diseases

What do we know about the role of gliotoxin in the pathobiology of Aspergillus fumigatus?

Kyung J. Kwon-Chung et al.

MEDICAL MYCOLOGY (2009)

Article Biochemical Research Methods

adegenet:: a R package for the multivariate analysis of genetic markers

Thibaut Jombart

BIOINFORMATICS (2008)

Review Mathematical & Computational Biology

Simultaneous inference in general parametric models

Torsten Hothorn et al.

BIOMETRICAL JOURNAL (2008)

Article Genetics & Heredity

Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae

Arnold B. Barton et al.

GENETICS (2008)

Article Biochemistry & Molecular Biology

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

Vardges Ter-Hovhannisyan et al.

GENOME RESEARCH (2008)

Article Genetics & Heredity

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

Natalie D. Fedorova et al.

PLOS GENETICS (2008)

Article Genetics & Heredity

PLINK: A tool set for whole-genome association and population-based linkage analyses

Shaun Purcell et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Computer Science, Interdisciplinary Applications

The ade4 package: Implementing the duality diagram for ecologists

Stephane Dray et al.

JOURNAL OF STATISTICAL SOFTWARE (2007)

Article Infectious Diseases

Multi-azole resistance in Aspergillus fumigatus

Susan J. Howard et al.

INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS (2006)

Article Microbiology

Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR

Lisa J. Griffiths et al.

JOURNAL OF MEDICAL MICROBIOLOGY (2006)

Review Cell Biology

The microbial pan-genome

D Medini et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2005)

Article Multidisciplinary Sciences

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:: Implications for the microbial pan-genome

H Tettelin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Review Microbiology

Aspergillus fumigatus:: saprophyte or pathogen?

F Tekaia et al.

CURRENT OPINION IN MICROBIOLOGY (2005)

Article Biochemistry & Molecular Biology

Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus

M Paoletti et al.

CURRENT BIOLOGY (2005)

Article Biochemistry & Molecular Biology

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints

M Stanke et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

HIERFSTAT, a package for R to compute and test hierarchical F-statistics

J Goudet

MOLECULAR ECOLOGY NOTES (2005)

Article Biochemical Research Methods

Automated generation of heuristics for biological sequence comparison

GS Slater et al.

BMC BIOINFORMATICS (2005)

Article Biochemical Research Methods

TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders

WH Majoros et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

A combined transmembrane topology and signal peptide prediction method

L Käll et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Immunology

Phagocytosis and intracellular fate of Aspergillus fumigatus conidia in alveolar macrophages

O Ibrahim-Granet et al.

INFECTION AND IMMUNITY (2003)

Review Microbiology

Aspergillus enzymes involved in degradation of plant cell wall polysaccharides

RP de Vries et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2001)