Comparative Genomics of the Pine Pathogens and Beetle Symbionts in the Genus Grosmannia

Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana)

(2013) Dawn E Hall et al.   BMC PLANT BIOLOGY

Deep phylogenetic divergence between Scolytoplatypus and Remansus, a new genus of Scolytoplatypodini from Madagascar (Coleoptera, Curculionidae, Scolytinae)

(2013) Bjarte Jordal   ZooKeys

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

Unequal Recombination and Evolution of the Mating-Type ( MAT ) Loci in the Pathogenic Fungus Grosmannia clavigera and Relatives

(2013) Clement K.-M. Tsui et al.   G3-Genes Genomes Genetics

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

(2013) Bradford J. Condon et al.   PLoS Genetics

Molecular phylogeny of bark and ambrosia beetles reveals multiple origins of fungus farming during periods of global warming

(2012) Bjarte H Jordal et al.   BMC EVOLUTIONARY BIOLOGY

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

(2012) Marina Marcet-Houben et al.   BMC GENOMICS

The cytochromes P450 of Grosmannia clavigera: Genome organization, phylogeny, and expression in response to pine host chemicals

(2012) Ljerka Lah et al.   FUNGAL GENETICS AND BIOLOGY

A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance toGrosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees

(2012) Ye Wang et al.   NEW PHYTOLOGIST

Evolution of Conifer Diterpene Synthases: Diterpene Resin Acid Biosynthesis in Lodgepole Pine and Jack Pine Involves Monofunctional and Bifunctional Diterpene Synthases

(2012) D. E. Hall et al.   PLANT PHYSIOLOGY

Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

(2012) Minfeng Xue et al.   PLoS Genetics

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

(2012) Pierre J. G. M. de Wit et al.   PLoS Genetics

genBlastG: using BLAST searches to build homologous gene models

(2011) Rong She et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Efficacy of tree defense physiology varies with bark beetle population density: a basis for positive feedback in eruptive species

(2011) Celia K. Boone et al.   CANADIAN JOURNAL OF FOREST RESEARCH

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

(2011) M. R. Andersen et al.   GENOME RESEARCH

A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes

(2011) Sajeet Haridas et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population structure and migration pattern of a conifer pathogen,Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle

(2011) CLEMENT K. M. TSUI et al.   MOLECULAR ECOLOGY

Mountain pine beetle host-range expansion threatens the boreal forest

(2011) CATHERINE I. CULLINGHAM et al.   MOLECULAR ECOLOGY

Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen Grosmannia clavigera

(2011) SEPIDEH M. ALAMOUTI et al.   MOLECULAR ECOLOGY

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

(2011) S. DiGuistini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

(2011) Weixin Wang et al.   Scientific Reports

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

(2011) Kevin McCluskey et al.   G3-Genes Genomes Genetics

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

(2011) Christopher A. Desjardins et al.   PLoS Genetics

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

(2011) Steven J. Klosterman et al.   PLoS Pathogens

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

(2011) James K Hane et al.   GENOME BIOLOGY

Facilitation in bark beetles: endemic mountain pine beetle gets a helping hand

(2010) Gregory D. Smith et al.   AGRICULTURAL AND FOREST ENTOMOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera

(2010) Uljana Hesse-Orce et al.   BMC GENOMICS

Phylogenetic analysis of fungal ABC transporters

(2010) Andriy Kovalchuk et al.   BMC GENOMICS

Differences in the constitutive terpene profile of lodgepole pine across a geographical range in British Columbia, and correlation with historical attack by mountain pine beetle

(2010) Erin L. Clark et al.   CANADIAN ENTOMOLOGIST

Comparative Genomics and the Evolution of Pathogenicity in Human Pathogenic Fungi

(2010) Gary P. Moran et al.   EUKARYOTIC CELL

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Positive Correlation between dN/dS and dS in Mammals Is Due to Runs of Adjacent Substitutions

(2010) Nina Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative phylogeography, genetic differentiation and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis

(2010) AMANDA D. ROE et al.   MOLECULAR ECOLOGY

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

(2010) G. AGUILETA et al.   MOLECULAR ECOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

(2010) Eva H. Stukenbrock et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Single sequence repeat markers reflect diversity and geographic barriers in Eurasian populations of the conifer pathogenCeratocystis polonica

(2009) M. Marin et al.   FOREST PATHOLOGY

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

(2009) Scott DiGuistini et al.   GENOME BIOLOGY

Genetic variation of piperidine alkaloids in Pinus ponderosa: a common garden study

(2008) Elizabeth A. Gerson et al.   ANNALS OF BOTANY

The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis

(2008) Stephen I. Wright et al.   Annual Review of Ecology Evolution and Systematics

The Origins of Plant Pathogens in Agro-Ecosystems

(2008) Eva H. Stukenbrock et al.   Annual Review of Phytopathology

AWclust: point-and-click software for non-parametric population structure analysis

(2008) Xiaoyi Gao et al.   BMC BIOINFORMATICS

Elongation Factor 3, EF3, Associates with the Calcium Channel Cch1 and Targets Cch1 to the Plasma Membrane inCryptococcus neoformans

(2008) Min Liu et al.   EUKARYOTIC CELL

“REVERSE ECOLOGY” AND THE POWER OF POPULATION GENOMICS

(2008) Yong Fuga Li et al.   EVOLUTION

Speciation in fungi

(2008) Tatiana Giraud et al.   FUNGAL GENETICS AND BIOLOGY

Autophagy in filamentous fungi

(2008) J POLLACK et al.   FUNGAL GENETICS AND BIOLOGY

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

(2008) R. Lambreghts et al.   GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Mountain pine beetle and forest carbon feedback to climate change

(2008) W. A. Kurz et al.   NATURE

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis

(2008) Darren M. Soanes et al.   PLoS One

Life history determines genetic structure and evolutionary potential of host–parasite interactions

(2008) Luke G. Barrett et al.   TRENDS IN ECOLOGY & EVOLUTION

The effect of domestication on the fungal proteome

(2008) Antonis Rokas   TRENDS IN GENETICS

Biosynthesis of secondary metabolites in the rice blast fungus Magnaporthe grisea: the role of hybrid PKS-NRPS in pathogenicity

(2007) Jérôme Collemare et al.