Hybridization and introgression drive genome evolution of Dutch elm disease pathogens

[1]  D. Petrov,et al.  Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans , 2018, Cell.

[2]  K. Chung,et al.  A Major Facilitator Superfamily Transporter Regulated by the Stress-Responsive Transcription Factor Yap1 Is Required for Resistance to Fungicides, Xenobiotics, and Oxidants and Full Virulence in Alternaria alternata , 2018, Front. Microbiol..

[3]  A. Fijarczyk,et al.  Balancing selection and introgression of newt immune-response genes , 2018, Proceedings of the Royal Society B: Biological Sciences.

[4]  Christophe Klopp,et al.  D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.

[5]  M. Fisher,et al.  Worldwide emergence of resistance to antifungal drugs challenges human health and food security , 2018, Science.

[6]  H. Rogers,et al.  The Molecular Nature Of The D-Factor in Ceratocystis Ulmi , 2018 .

[7]  Brian Bushnell,et al.  BBMerge – Accurate paired shotgun read merging via overlap , 2017, PloS one.

[8]  C. Landry,et al.  The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species , 2017, Molecular biology and evolution.

[9]  E. Stukenbrock,et al.  Evolution and genome architecture in fungal plant pathogens , 2017, Nature Reviews Microbiology.

[10]  R. Hamelin,et al.  Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts , 2017, Molecular ecology.

[11]  T. Hsiang,et al.  A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles. , 2017, Fungal biology.

[12]  L. Bernier,et al.  From yeast to hypha: defining transcriptomic signatures of the morphological switch in the dimorphic fungal pathogen Ophiostoma novo-ulmi , 2016, BMC Genomics.

[13]  A. Estoup,et al.  Is There a Genetic Paradox of Biological Invasion , 2016 .

[14]  Simon H. Martin,et al.  Exploring Evolutionary Relationships Across the Genome Using Topology Weighting , 2016, Genetics.

[15]  B. Thomma,et al.  Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. , 2016, Current opinion in microbiology.

[16]  Yongze Yuan,et al.  A novel major facilitator superfamily transporter in Penicillium digitatum (PdMFS2) is required for prochloraz resistance, conidiation and full virulence , 2016, Biotechnology Letters.

[17]  Jana Sperschneider,et al.  EffectorP: predicting fungal effector proteins from secretomes using machine learning. , 2016, The New phytologist.

[18]  Dominique Sanglard,et al.  Emerging Threats in Antifungal-Resistant Fungal Pathogens , 2016, Front. Med..

[19]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[20]  E. Stukenbrock The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens. , 2016, Phytopathology.

[21]  A. Riba,et al.  Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species , 2016, Nature Genetics.

[22]  C. Landry,et al.  RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi , 2015, G3: Genes, Genomes, Genetics.

[23]  T. Giraud,et al.  The population biology of fungal invasions , 2015, Molecular ecology.

[24]  G. Gauthier Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects , 2015, PLoS pathogens.

[25]  B. Henrissat,et al.  Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease , 2014, Genome biology and evolution.

[26]  Ryan M. Layer,et al.  SpeedSeq: Ultra-fast personal genome analysis and interpretation , 2014, Nature Methods.

[27]  Anders Albrechtsen,et al.  ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.

[28]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[29]  L. Bernier,et al.  A rapid virulence assay for the Dutch elm disease fungus Ophiostoma novo‐ulmi by inoculation of apple (Malus × domestica ‘Golden Delicious’) fruits , 2014 .

[30]  Matteo Fumagalli,et al.  ngsTools: methods for population genetics analyses from next-generation sequencing data , 2014, Bioinform..

[31]  K. Chung,et al.  Resistance to oxidative stress via regulating siderophore-mediated iron acquisition by the citrus fungal pathogen Alternaria alternata. , 2014, Microbiology.

[32]  M. Lercher,et al.  PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R , 2014, Molecular biology and evolution.

[33]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[34]  D. Nuss,et al.  Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus , 2014, Genetics.

[35]  Eric Bazin,et al.  The effect of mating system on invasiveness: some genetic load may be advantageous when invading new environments , 2014, Biological Invasions.

[36]  Ira M. Hall,et al.  SAMBLASTER: fast duplicate marking and structural variant read extraction , 2014, Bioinform..

[37]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[38]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[39]  Jin-Rong Xu,et al.  Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi , 2014, BMC Genomics.

[40]  Jin-Rong Xu,et al.  Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi , 2013, BMC Genomics.

[41]  K. Dewar,et al.  Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. , 2013, Journal of biomolecular techniques : JBT.

[42]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[43]  James G. Booth,et al.  SnIPRE: Selection Inference Using a Poisson Random Effects Model , 2012, PLoS Comput. Biol..

[44]  Ryan M. Layer,et al.  LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.

[45]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[46]  J. Brownstein,et al.  Emerging fungal threats to animal, plant and ecosystem health , 2012, Nature.

[47]  Inna Dubchak,et al.  The Genome Portal of the Department of Energy Joint Genome Institute , 2011, Nucleic Acids Res..

[48]  Thibaut Jombart,et al.  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data , 2011, Bioinform..

[49]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[50]  David Reich,et al.  Testing for ancient admixture between closely related populations. , 2011, Molecular biology and evolution.

[51]  D. Makowski,et al.  Predicting invasion success of forest pathogenic fungi from species traits , 2011 .

[52]  M. Gerstein,et al.  CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.

[53]  Steven J. M. Jones,et al.  Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen , 2011, Proceedings of the National Academy of Sciences.

[54]  Asan,et al.  Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude , 2010, Science.

[55]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[56]  Wolfgang Huber,et al.  EBImage—an R package for image processing with applications to cellular phenotypes , 2010, Bioinform..

[57]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[58]  C. Brasier,et al.  Rapid emergence of hybrids between the two subspecies of Ophiostoma novo‐ulmi with a high level of pathogenic fitness , 2010 .

[59]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[60]  C. Bochet,et al.  The ABC transporter BcatrB from Botrytis cinerea exports camalexin and is a virulence factor on Arabidopsis thaliana. , 2009, The Plant journal : for cell and molecular biology.

[61]  David Turrà,et al.  Identification of a new biocontrol gene in Trichoderma atroviride: the role of an ABC transporter membrane pump in the interaction with different plant-pathogenic fungi. , 2009, Molecular plant-microbe interactions : MPMI.

[62]  Himanshu Sinha,et al.  Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast , 2008, Genetics.

[63]  Thibaut Jombart,et al.  adegenet: a R package for the multivariate analysis of genetic markers , 2008, Bioinform..

[64]  P M Bennett,et al.  Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria , 2008, British journal of pharmacology.

[65]  I. Sache,et al.  The fungal dimension of biological invasions. , 2007, Trends in ecology & evolution.

[66]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[67]  Noah A. Rosenberg,et al.  CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure , 2007, Bioinform..

[68]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[69]  C. Brasier,et al.  Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo‐ulmi , 2005, Molecular ecology.

[70]  Casey M. Bergman,et al.  Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..

[71]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[72]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[73]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[74]  C. Schardl,et al.  Interspecific hybridization in plant‐associated fungi and oomycetes: a review , 2003, Molecular ecology.

[75]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[76]  J. Stenlid,et al.  Pathogenic fungal species hybrids infecting plants. , 2002, Microbes and infection.

[77]  E. Wagner,et al.  Proteome analysis of Aspergillus nidulans reveals proteins associated with the response to the antibiotic concanamycin A, produced by Streptomyces species , 2002, Molecular Genetics and Genomics.

[78]  T. Kirisits,et al.  Genetic evidence for natural hybridization between the Dutch elm disease pathogens Ophiostoma novo-ulmi ssp. novo-ulmi and O. novo-ulmi ssp. americana , 2002 .

[79]  C. Brasier,et al.  Designation of the EAN and NAN races of Ophiostoma novo-ulmi as subspecies , 2001 .

[80]  N. Barton The role of hybridization in evolution , 2001, Molecular ecology.

[81]  C. Brasier Rapid Evolution of Introduced Plant Pathogens via Interspecific Hybridization , 2001 .

[82]  C. Brasier,et al.  Survival of clones of NAN Ophiostoma novo-ulmi around its probable centre of appearance in North America , 2000 .

[83]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[84]  C. Brasier Plant pathology: The rise of the hybrid fungi , 2000, Nature.

[85]  M. Milgroom,et al.  POTENTIAL DIVERSITY IN VEGETATIVE COMPATIBILITY TYPES OF OPHIOSTOMA NOVO-ULMI IN NORTH AMERICA , 1997 .

[86]  C. Brasier Low genetic diversity of the Ophiostoma novo-ulmi population in North America. , 1996 .

[87]  C. Brasier,et al.  Molecular relationships between Ophiostoma ulmi and the NAN and EAN races of O. novo-ulmi determined by RAPD markers , 1995 .

[88]  M. D. Mehrotra,et al.  Ophiostoma himal-ulmi sp. nov., a new species of Dutch elm disease fungus endemic to the Himalayas , 1995 .

[89]  R. Proctor,et al.  Lack of association between tolerance to the elm phytoalexin mansonone E and virulence in Ophiostoma novo-ulmi , 1994 .

[90]  C. Brasier,et al.  Contrasting structure of European and North American populations of Ophiostoma ulmi , 1994 .

[91]  C. Brasier,et al.  Molecular relationships between Ophiostoma ulmi and the NAN and EAN races of O. novo-ulmi determined by restriction fragment length polymorphisms of nuclear DNA , 1993 .

[92]  C. Brasier,et al.  Ophiostoma novo-ulmi sp. nov., causative agent of current Dutch elm disease pandemics , 1991, Mycopathologia.

[93]  M. Kreitman,et al.  Adaptive protein evolution at the Adh locus in Drosophila , 1991, Nature.

[94]  L. Bernier,et al.  Mutations in Ophiostoma ulmi induced by N-methyl-N′-nitro-N-nitrosoguanidine , 1990 .

[95]  C. Brasier Rapid changes in genetic structure of epidemic populations of Ophiostoma ulmi , 1988, Nature.

[96]  C. Brasier Comparison of pathogencity and cultural characteristics in the EAN and NAN aggressive subgroups of Ophiostoma ulmi , 1986 .

[97]  P. Pukkila,et al.  Inheritance of DNA methylation in Coprinus cinereus , 1986, Molecular and cellular biology.

[98]  L. Duchesne,et al.  Accumulation of phytoalexins in Ulmus americana in response to infection by a nonaggressive and an aggressive strain of Ophiostoma ulmi , 1985 .

[99]  C. Brasier A cytoplasmically transmitted disease of Ceratocystis ulmi , 1983, Nature.

[100]  C. Brasier,et al.  The aggressive and non-aggressive strains of Ceratocystis ulmi have different temperature optima for growth , 1981 .

[101]  C. Brasier Inheritance of pathogenicity and cultural characters in Ceratocystis ulmi; hybridization of protoperithecial and non-aggressive strains , 1977 .

[102]  H. Akaike A new look at the statistical model identification , 1974 .

[103]  C. Brasier,et al.  Correlation between Cultural Characters and Pathogenicity in Ceratocystis ulmi from Britain, Europe and America , 1973, Nature.

[104]  J. Overeem,et al.  Accumulation of mansonones E and F in Ulmus hollandica infected with Ceratocystis ulmi. , 1970 .

[105]  L. Bernier,et al.  Ophiostoma ulmi DNA naturally introgressed into an isolate of Ophiostoma novo-ulmi is clustered around pathogenicity and mating type loci , 2019, Phytoprotection.

[106]  Ole Tange,et al.  GNU Parallel: The Command-Line Power Tool , 2011, login Usenix Mag..

[107]  Sequence analysis Advance Access publication June 7, 2011 The variant call format and VCFtools , 2010 .

[108]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[109]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[110]  C. J. Eades Characterization of the alpha-mannosidase gene family in filamentous fungi , 2001 .

[111]  L. Bernier,et al.  Localization of a Pathogenicity Gene in Ophiostoma novo-ulmi and Evidence That It May Be Introgressed from O. ulmi , 1999 .

[112]  C. Brasier,et al.  Rare interspecific hybrids in natural populations of the Dutch elm disease pathogens Ophiostoma ulmi and O. novo-ulmi. , 1998 .

[113]  Genshiro Kitagawa,et al.  Selected papers of Hirotugu Akaike , 1998 .

[114]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[115]  C. Brasier The population biology of Dutch elm disease: its principle features and some implications for other host-pathogen systems. , 1986 .

[116]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .