Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum

[1]  M. Frąc,et al.  Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops—A Review , 2019, Molecules.

[2]  Arne Schwelm,et al.  Detection of Verticillium species in Swedish soils using real-time PCR , 2017, Archives of Microbiology.

[3]  Michael F. Seidl,et al.  A previously established divergent lineage of the hybrid fungal pathogen Verticillium longisporum emerges as stem striping pathogen in British oilseed rape , 2017, bioRxiv.

[4]  Irina S Druzhinina,et al.  Several steps of lateral gene transfer followed by events of ‘birth-and-death’ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster , 2016, BMC Evolutionary Biology.

[5]  B. Thomma,et al.  Verticillium longisporum, the invisible threat to oilseed rape and other brassicaceous plant hosts. , 2016, Molecular plant pathology.

[6]  G. Coaker,et al.  Plant-Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners. , 2016, Annual review of phytopathology.

[7]  Michael F. Seidl,et al.  Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. , 2016, Current opinion in microbiology.

[8]  Leszek P. Pryszcz,et al.  The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis , 2015, PLoS genetics.

[9]  M. Koch,et al.  A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History[OPEN] , 2015, Plant Cell.

[10]  Michael F. Seidl,et al.  Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome , 2015, mBio.

[11]  Toni Gabaldón,et al.  Redundans: an assembly pipeline for highly heterozygous genomes , 2015, Nucleic acids research.

[12]  P. Inderbitzin,et al.  The Three Lineages of the Diploid Hybrid Verticillium longisporum Differ in Virulence and Pathogenicity. , 2015, Phytopathology.

[13]  Hanhong Bae,et al.  The diversity of fungal genome , 2015, Biological Procedures Online.

[14]  Michael F. Seidl,et al.  The Genome of the Saprophytic Fungus Verticillium tricorpus Reveals a Complex Effector Repertoire Resembling That of Its Pathogenic Relatives. , 2015, Molecular plant-microbe interactions : MPMI.

[15]  P. Inderbitzin,et al.  Maintenance of Sex-Related Genes and the Co-Occurrence of Both Mating Types in Verticillium dahliae , 2014, PloS one.

[16]  Rangel C. Souza,et al.  Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis , 2014, BMC Genomics.

[17]  H. Mewes,et al.  The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer , 2014, PloS one.

[18]  N. L. Glass,et al.  Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi. , 2014, Annual review of phytopathology.

[19]  Wayne E. Clarke,et al.  Polyploid Evolution of the Brassicaceae during the Cenozoic Era[C][W][OPEN] , 2014, Plant Cell.

[20]  P. Inderbitzin,et al.  Verticillium systematics and evolution: how confusion impedes Verticillium wilt management and how to resolve it. , 2014, Phytopathology.

[21]  Leszek P. Pryszcz,et al.  Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies , 2014, Genome biology and evolution.

[22]  Jinlong Wang,et al.  Molecular characterization and functional analysis of a specific secreted protein from highly virulent defoliating Verticillium dahliae. , 2013, Gene.

[23]  Jaeyoung Choi,et al.  Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes , 2013, BMC Genomics.

[24]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[25]  L. Franková,et al.  Biochemistry and physiological roles of enzymes that 'cut and paste' plant cell-wall polysaccharides. , 2013, Journal of experimental botany.

[26]  B. Thomma,et al.  Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen , 2013, Genome research.

[27]  P. Inderbitzin,et al.  Identification and Differentiation of Verticillium Species and V. longisporum Lineages by Simplex and Multiplex PCR Assays , 2013, PloS one.

[28]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

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

[30]  B. Thomma,et al.  Evidence for functional diversification within a fungal NEP1-like protein family. , 2013, Molecular plant-microbe interactions : MPMI.

[31]  B. Dujon,et al.  Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts , 2012, Microbiology and Molecular Reviews.

[32]  Travis C Glenn,et al.  Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.

[33]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[34]  S. Klosterman,et al.  Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification , 2012, BMC Genomics.

[35]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[36]  P. Cannon,et al.  Lectera, a new genus of the Plectosphaerellaceae for the legume pathogen Volutella colletotrichoides , 2012 .

[37]  Paul P Jung,et al.  Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization , 2012, G3: Genes | Genomes | Genetics.

[38]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[39]  A. Künstner,et al.  ConDeTri - A Content Dependent Read Trimmer for Illumina Data , 2011, PloS one.

[40]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[41]  Christina A. Cuomo,et al.  Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens , 2011, PLoS pathogens.

[42]  P. Inderbitzin,et al.  The Ascomycete Verticillium longisporum Is a Hybrid and a Plant Pathogen with an Expanded Host Range , 2011, PloS one.

[43]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[44]  D. Ripoll,et al.  Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution , 2010, PloS one.

[45]  David R. Kelley,et al.  Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.

[46]  S. Revankar,et al.  Melanized Fungi in Human Disease , 2010, Clinical Microbiology Reviews.

[47]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[48]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[49]  Richard M. Clark,et al.  The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana , 2010, Science.

[50]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[51]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[52]  J. Heitman,et al.  Identification of the sex genes in an early diverged fungus , 2008, Nature.

[53]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[54]  R. Zare Gibellulopsis, a suitable genus for Verticillium nigrescens, and Musicillium, a new genus for V. theobromae , 2007 .

[55]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

[56]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[57]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[58]  M. Gijzen,et al.  Nep1-Like Proteins from Plant Pathogens: Recruitment and Diversification of the NPP1 Domain Across Taxa , 2006 .

[59]  A. Johansson,et al.  Early responses in the Arabidopsis-Verticillium longisporum pathosystem are dependent on NDR1, JA- and ET-associated signals via cytosolic NPR1 and RFO1. , 2006, Molecular plant-microbe interactions : MPMI.

[60]  F. Dromer,et al.  Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. , 2006, FEMS yeast research.

[61]  B. Thomma,et al.  Physiology and molecular aspects of Verticillium wilt diseases caused by V. dahliae and V. albo-atrum. , 2006, Molecular plant pathology.

[62]  A. Johansson,et al.  Plant Host Range of Verticillium longisporum and Microsclerotia Density in Swedish Soils , 2006, European Journal of Plant Pathology.

[63]  M. Borodovsky,et al.  Gene identification in novel eukaryotic genomes by self-training algorithm , 2005, Nucleic acids research.

[64]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[65]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[66]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[67]  Burkhard Morgenstern,et al.  AUGUSTUS: a web server for gene finding in eukaryotes , 2004, Nucleic Acids Res..

[68]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[69]  C. Dixelius,et al.  Phylogenetic analysis of Verticillium species based on nuclear and mitochondrial sequences , 2004, Archives of Microbiology.

[70]  U. Lagercrantz,et al.  Estimation of Genetic Variation Among Verticillium Isolates using AFLP Analysis , 2003, European Journal of Plant Pathology.

[71]  C. Dixelius,et al.  Identification of the causal agent of Verticillium wilt of winter oilseed rape in Sweden, V. longisporum , 2002 .

[72]  A. Tiedemann,et al.  Morphological and Physiological Differentiation among Vegetative Compatibility Groups of Verticillium dahliae in Relation to V. longisporum , 2001 .

[73]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[74]  B. Bainbridge,et al.  Morphological and molecular characterization of Verticillium longisporum comb. nov., pathogenic to oilseed rape , 1997 .

[75]  R. Metzenberg,et al.  Mating type and mating strategies in Neurospora , 1990, BioEssays : news and reviews in molecular, cellular and developmental biology.

[76]  J. B. Heale,et al.  Relationship between DNA Content and Spore Volume in Sixteen Isolates of Verticillium lecanii and Two New Diploids of V. dahliae (= V. dahliae var. longisporum Stark) , 1985 .

[77]  J. Heitman,et al.  Is sex necessary? , 1961, BMC Biology.

[78]  Guy N. Brock,et al.  Biological impact of missing-value imputation on downstream analyses of gene expression profiles , 2011, Bioinform..

[79]  J. R. Lobry,et al.  SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis , 2007 .