Evolution and comparative genomics of the most common Trichoderma species

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

(2018) Irina S. Druzhinina et al.   PLoS Genetics

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(2017)   SYSTEMATIC BIOLOGY

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi

(2017) Juan Li et al.   Scientific Reports

Fungal lifestyle reflected in serine protease repertoire

(2017) Anna Muszewska et al.   Scientific Reports

Regulation and Role of Fungal Secondary Metabolites

(2016) Juliane Macheleidt et al.   Annual Review of Genetics

A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness

(2016) Irina S. Druzhinina et al.   Biotechnology for Biofuels

CAZyme content of Pochonia chlamydosporia reflects that chitin and chitosan modification are involved in nematode parasitism

(2016) Almudena Aranda-Martinez et al.   ENVIRONMENTAL MICROBIOLOGY

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

(2016) Monika Schmoll et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response

(2016) Marina Lamacchia et al.   Frontiers in Microbiology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots

(2015) Maria E Morán-Diez et al.   BMC GENOMICS

Sm2, a paralog of the Trichoderma cerato-platanin elicitor Sm1, is also highly important for plant protection conferred by the fungal-root interaction of Trichoderma with maize

(2015) Romana Gaderer et al.   BMC MICROBIOLOGY

Molecular diversity of LysM carbohydrate-binding motifs in fungi

(2015) Gunseli Bayram Akcapinar et al.   CURRENT GENETICS

Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains

(2015) Priscila Chaverri et al.   MYCOLOGIA

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia

(2015) W.M. Jaklitsch et al.   STUDIES IN MYCOLOGY

Cerato-platanins: a fungal protein family with intriguing properties and application potential

(2014) Romana Gaderer et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum

(2014) Andrei Steindorff et al.   BMC GENOMICS

Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style

(2014) Bin-Bin Xie et al.   Genome Biology and Evolution

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Strong Genome-Wide Selection Early in the Evolution of Prochlorococcus Resulted in a Reduced Genome through the Loss of a Large Number of Small Effect Genes

(2014) Zhiyi Sun et al.   PLoS One

Independent Expansion of Zincin Metalloproteinases in Onygenales Fungi May Be Associated with Their Pathogenicity

(2014) Juan Li et al.   PLoS One

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

(2013) Robert Bischof et al.   Biotechnology for Biofuels

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

(2013) Lothar Wissler et al.   Genome Biology and Evolution

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics

(2013) David J. Studholme et al.   Frontiers in Plant Science

l-xylo-3-Hexulose Reductase Is the Missing Link in the Oxidoreductive Pathway for d-Galactose Catabolism in Filamentous Fungi

(2012) Dominik Mojzita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sexual selection in fungi

(2012) B. P. S. Nieuwenhuis et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Origin and evolution of carnivorism in the Ascomycota (fungi)

(2012) E. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fungal arabinan and l-arabinose metabolism

(2011) Bernhard Seiboth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Causes and Consequences of Genome Expansion in Fungi

(2011) Yogeshwar D. Kelkar et al.   Genome Biology and Evolution

Secondary metabolism in Trichoderma - a genomic perspective

(2011) P. K. Mukherjee et al.   MICROBIOLOGY-SGM

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Trichoderma: the genomics of opportunistic success

(2011) Irina S. Druzhinina et al.   NATURE REVIEWS MICROBIOLOGY

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

(2011) Christian P Kubicek et al.   GENOME BIOLOGY

The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages

(2010) Irina S Druzhinina et al.   BMC EVOLUTIONARY BIOLOGY

Evolution and Ecophysiology of the Industrial Producer Hypocrea jecorina (Anamorph Trichoderma reesei) and a New Sympatric Agamospecies Related to It

(2010) Irina S. Druzhinina et al.   PLoS One

European species of Hypocrea Part I. The green-spored species

(2010) Walter M. Jaklitsch   STUDIES IN MYCOLOGY

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

Fungal incompatibility: Evolutionary origin in pathogen defense?

(2009) Mathieu Paoletti et al.   BIOESSAYS

Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family

(2009) Damien Chevanne et al.   CURRENT GENETICS

Deccan volcanism, the KT mass extinction and dinosaurs

(2009) G. Keller et al.   JOURNAL OF BIOSCIENCES

Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa

(2009) Takao Kasuga et al.   PLoS One

The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal–arthropod symbioses

(2008) Gi-Ho Sung et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY