The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum

(2014) Rahul Sharma et al.   Genome Biology and Evolution

Genome and Transcriptome Analysis of the Basidiomycetous Yeast Pseudozyma antarctica Producing Extracellular Glycolipids, Mannosylerythritol Lipids

(2014) Tomotake Morita et al.   PLoS One

Functional Characterization of the Xanthophyllomyces dendrorhous Farnesyl Pyrophosphate Synthase and Geranylgeranyl Pyrophosphate Synthase Encoding Genes That Are Involved in the Synthesis of Isoprenoid Precursors

(2014) Jennifer Alcaíno et al.   PLoS One

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

(2014) Guilhem Janbon et al.   PLoS Genetics

Genetic engineering of the complete carotenoid pathway towards enhanced astaxanthin formation in Xanthophyllomyces dendrorhous starting from a high-yield mutant

(2013) Sören Gassel et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent

(2013) Janja Zajc et al.   BMC GENOMICS

Production of α-cuprenene in Xanthophyllomyces dendrorhous: a step closer to a potent terpene biofactory

(2013) Elena Melillo et al.   Microbial Cell Factories

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

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

Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe

(2013) Márcia David-Palma et al.   MOLECULAR ECOLOGY

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogenMixia osmundae

(2013) Merje Toome et al.   NEW PHYTOLOGIST

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Enhancement of carotenoid production by disrupting the C22-sterol desaturase gene (CYP61) in Xanthophyllomyces dendrorhous

(2012) Iris Loto et al.   BMC MICROBIOLOGY

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

(2012) Mahajabeen Padamsee et al.   FUNGAL GENETICS AND BIOLOGY

Cell-to-cell communication in plants, animals, and fungi: a comparative review

(2012) Sandra Bloemendal et al.   NATURWISSENSCHAFTEN

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)

(2011) Ana M. Millanes et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Functional Analysis of the Phycomyces carRA Gene Encoding the Enzymes Phytoene Synthase and Lycopene Cyclase

(2011) Catalina Sanz et al.   PLoS One

Engineering of geranylgeranyl pyrophosphate synthase levels and physiological conditions for enhanced carotenoid and astaxanthin synthesis in Xanthophyllomyces dendrorhous

(2010) Jürgen Breitenbach et al.   BIOTECHNOLOGY LETTERS

Differential carotenoid production and gene expression in Xanthophyllomyces dendrorhous grown in a nonfermentable carbon source

(2010) Aniela Wozniak et al.   FEMS YEAST RESEARCH

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Phylogenetic Distribution of Fungal Sterols

(2010) John D. Weete et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fatty acid metabolism in the ectomycorrhizal fungusLaccaria bicolor

(2009) Marlis Reich et al.   NEW PHYTOLOGIST

Cloning of the cytochrome p450 reductase (crtR) gene and its involvement in the astaxanthin biosynthesis of Xanthophyllomyces dendrorhous

(2008) Jennifer Alcaíno et al.   BMC MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY