Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi.

Abstract:

BACKGROUND:Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. RESULTS:97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. CONCLUSIONS:Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.

journal_name

Genome Biol

journal_title

Genome biology

authors

Burmester A,Shelest E,Glöckner G,Heddergott C,Schindler S,Staib P,Heidel A,Felder M,Petzold A,Szafranski K,Feuermann M,Pedruzzi I,Priebe S,Groth M,Winkler R,Li W,Kniemeyer O,Schroeckh V,Hertweck C,Hube B,White TC

doi

10.1186/gb-2011-12-1-r7

subject

Has Abstract

pub_date

2011-01-01 00:00:00

pages

R7

issue

1

eissn

1474-7596

issn

1474-760X

pii

gb-2011-12-1-r7

journal_volume

12

pub_type

杂志文章
  • Searching for SNPs with cloud computing.

    abstract::As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-11-r134

    authors: Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

    更新日期:2009-01-01 00:00:00

  • The R-spondin protein family.

    abstract::The four vertebrate R-spondin proteins are secreted agonists of the canonical Wnt/β-catenin signaling pathway. These proteins are approximately 35 kDa, and are characterized by two amino-terminal furin-like repeats, which are necessary and sufficient for Wnt signal potentiation, and a thrombospondin domain situated mo...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2012-13-3-242

    authors: de Lau WB,Snel B,Clevers HC

    更新日期:2012-01-01 00:00:00

  • Epigenetic modifications of histones in cancer.

    abstract::The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we revie...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/s13059-019-1870-5

    authors: Zhao Z,Shilatifard A

    更新日期:2019-11-20 00:00:00

  • Selection in the evolution of gene duplications.

    abstract:BACKGROUND:Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolut...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-2-research0008

    authors: Kondrashov FA,Rogozin IB,Wolf YI,Koonin EV

    更新日期:2002-01-01 00:00:00

  • Wrangling for microRNAs provokes much crosstalk.

    abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-11-132

    authors: Marques AC,Tan J,Ponting CP

    更新日期:2011-11-21 00:00:00

  • Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences.

    abstract:BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-6-r87

    authors: Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

    更新日期:2014-06-30 00:00:00

  • Consistent probabilistic outputs for protein function prediction.

    abstract::In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-s1-s6

    authors: Obozinski G,Lanckriet G,Grant C,Jordan MI,Noble WS

    更新日期:2008-01-01 00:00:00

  • PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.

    abstract::The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1364-2

    authors: Krakau S,Richard H,Marsico A

    更新日期:2017-12-28 00:00:00

  • Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.

    abstract:BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-9-research0051

    authors: Xie G,Bonner CA,Jensen RA

    更新日期:2002-08-29 00:00:00

  • Genomes of uncultured eukaryotes: sorting FACS from fiction.

    abstract::A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-6-117

    authors: Worden AZ,Dupont C,Allen AE

    更新日期:2011-06-27 00:00:00

  • In silico meets in vivo.

    abstract::A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2008-9-2-302

    authors: Weng Z,Guigó R

    更新日期:2008-01-01 00:00:00

  • DNA methylation and epigenomics: new technologies and emerging concepts.

    abstract::A report of the Keystone Symposia joint meetings on DNA Methylation and Epigenomics held in Keystone, Colorado, USA, 29 March to 3 April, 2015. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0674-5

    authors: Chatterjee A,Eccles MR

    更新日期:2015-05-21 00:00:00

  • Global orchestration of gene expression by the biological clock of cyanobacteria.

    abstract::Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2004-5-4-217

    authors: Johnson CH

    更新日期:2004-01-01 00:00:00

  • Chemical genomics in yeast.

    abstract::Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2004-5-9-240

    authors: Brenner C

    更新日期:2004-01-01 00:00:00

  • Exploiting microarrays to reveal differential gene expression in the nervous system.

    abstract::Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differen...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-2-105

    authors: Griffin RS,Mills CD,Costigan M,Woolf CJ

    更新日期:2003-01-01 00:00:00

  • Accelerating research through reagent repositories: the genome editing example.

    abstract::Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...

    journal_title:Genome biology

    pub_type: 面试

    doi:10.1186/s13059-015-0830-y

    authors: Joung JK,Voytas DF,Kamens J

    更新日期:2015-11-20 00:00:00

  • Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

    abstract::Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0706-1

    authors: Fan X,Zhang X,Wu X,Guo H,Hu Y,Tang F,Huang Y

    更新日期:2015-07-23 00:00:00

  • Intraepithelial gamma delta T cells exposed by functional genomics.

    abstract::Epithelial tissues house gammadelta T cells, which are important for the mucosal immune system and may be involved in controlling malignancies, infections and inflammation. Whole-genome gene-expression analysis provides a new way to study the signals required for the activation of gammadelta T cells, their mode of act...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2001-2-11-reviews1031

    authors: Boismenu R,Havran WL

    更新日期:2001-01-01 00:00:00

  • Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver.

    abstract:BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-6-r79

    authors: Blanc V,Park E,Schaefer S,Miller M,Lin Y,Kennedy S,Billing AM,Ben Hamidane H,Graumann J,Mortazavi A,Nadeau JH,Davidson NO

    更新日期:2014-06-19 00:00:00

  • mirMark: a site-level and UTR-level classifier for miRNA target prediction.

    abstract::MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0500-5

    authors: Menor M,Ching T,Zhu X,Garmire D,Garmire LX

    更新日期:2014-01-01 00:00:00

  • Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments.

    abstract:BACKGROUND:Methods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. Here we present a flexible, quantitative Bayesian framewor...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-12-research0071

    authors: Townsend JP,Hartl DL

    更新日期:2002-01-01 00:00:00

  • Design and computational analysis of single-cell RNA-sequencing experiments.

    abstract::Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/s13059-016-0927-y

    authors: Bacher R,Kendziorski C

    更新日期:2016-04-07 00:00:00

  • Permutation-validated principal components analysis of microarray data.

    abstract:BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-4-research0019

    authors: Landgrebe J,Wurst W,Welzl G

    更新日期:2002-01-01 00:00:00

  • EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

    abstract::The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-2-r14

    authors: Bock C,Halachev K,Büch J,Lengauer T

    更新日期:2009-02-10 00:00:00

  • Domain atrophy creates rare cases of functional partial protein domains.

    abstract:BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0655-8

    authors: Prakash A,Bateman A

    更新日期:2015-04-30 00:00:00

  • The Smads.

    abstract:SUMMARY:The large transforming growth factor-beta (TGFbeta) superfamily of secreted proteins regulate the growth, development and differentiation of cells in diverse organisms, including nematode worms, flies, mice and humans. Signals are initiated upon binding of TGFbeta superfamily members to cell-surface serine/thre...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2001-2-8-reviews3010

    authors: Attisano L,Lee-Hoeflich ST

    更新日期:2001-01-01 00:00:00

  • The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles.

    abstract:BACKGROUND:Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell signaling, movement and multicellular development. Ras guanine-nucleotide exchange factors (RasGEFs) are the proteins that activate Ras...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-8-r68

    authors: Wilkins A,Szafranski K,Fraser DJ,Bakthavatsalam D,Müller R,Fisher PR,Glöckner G,Eichinger L,Noegel AA,Insall RH

    更新日期:2005-01-01 00:00:00

  • SAGE profiling of the forelimb and hindlimb.

    abstract::A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2002-3-3-reviews1007

    authors: Logan M

    更新日期:2002-01-01 00:00:00

  • Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.

    abstract:BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2004-5-2-r10

    authors: Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

    更新日期:2004-01-01 00:00:00

  • Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans.

    abstract:BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-7-r75

    authors: Katju V,Farslow JC,Bergthorsson U

    更新日期:2009-01-01 00:00:00