CRISPR/Cas9-mediated deletion of large chromosomal segments identifies a minichromosome modulating the Colletotrichum graminicola virulence on maize.

[1]  You-Liang Peng,et al.  Molecular Genetics of Anthracnose Resistance in Maize , 2022, Journal of fungi.

[2]  H. Burbano,et al.  Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus , 2021, PLoS genetics.

[3]  M. Thon,et al.  Genome Sequence Resources of Colletotrichum truncatum, C. plurivorum, C. musicola and C. sojae: Four Species Pathogenic to Soybean (Glycine max). , 2020, Phytopathology.

[4]  Fang-fang Fu,et al.  Genome sequence and comparative analysis of Colletotrichum gloeosporioides isolated from Liriodendron leaves. , 2020, Phytopathology.

[5]  B. Liu,et al.  Transcriptome Analysis and Identification of Genes Associated with Starch Metabolism in Castanea henryi Seed (Fagaceae) , 2020, International journal of molecular sciences.

[6]  Damon L. Smith,et al.  Corn Yield Loss Estimates Due to Diseases in the United States and Ontario, Canada, from 2016 to 2019 , 2020, Plant Health Progress.

[7]  Y. Narusaka,et al.  Genome sequence resources for four phytopathogenic fungi from the Colletotrichum orbiculare species complex. , 2019, Molecular plant-microbe interactions : MPMI.

[8]  C. Duan,et al.  First Report of Anthracnose Leaf Blight of Maize Caused by Colletotrichum graminicola in China , 2019, Plant Disease.

[9]  C. Pozniak,et al.  Genetic map‐guided genome assembly reveals a virulence‐governing minichromosome in the lentil anthracnose pathogen Colletotrichum lentis , 2018, The New phytologist.

[10]  Sanzhen Liu,et al.  Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus , 2018, bioRxiv.

[11]  L. Taher,et al.  A Dispensable Chromosome Is Required for Virulence in the Hemibiotrophic Plant Pathogen Colletotrichum higginsianum , 2018, Front. Microbiol..

[12]  Jian Wang,et al.  SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data , 2017, GigaScience.

[13]  D. Schwartz,et al.  Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters , 2017, BMC Genomics.

[14]  A. Kovařík,et al.  B-chrom: a database on B-chromosomes of plants, animals and fungi. , 2017, The New phytologist.

[15]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[16]  T. Arie,et al.  Tailor‐made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus , 2015, Biotechnology and bioengineering.

[17]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[18]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[19]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[20]  S. Schaffert,et al.  Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells. , 2014, BioTechniques.

[21]  Xingxu Huang,et al.  sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites , 2014, PloS one.

[22]  W. Pirovano,et al.  SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information , 2014, BMC Bioinformatics.

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

[24]  Hui Zhao,et al.  Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis , 2014, Development.

[25]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[26]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[27]  Neil Moore,et al.  Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses , 2012, Nature Genetics.

[28]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[29]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[30]  G. Rech,et al.  Plant Defense Mechanisms Are Activated during Biotrophic and Necrotrophic Development of Colletotricum graminicola in Maize1[W][OA] , 2012, Plant Physiology.

[31]  Jeffrey J. Coleman,et al.  Characterization of the gene encoding pisatin demethylase (FoPDA1) in Fusarium oxysporum. , 2011, Molecular plant-microbe interactions : MPMI.

[32]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[33]  Wing-Kin Sung,et al.  A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence , 2010, PLoS pathogens.

[34]  V. Bhadauria,et al.  Dual trypan-aniline blue fluorescence staining methods for studying fungus-plant interactions , 2010 .

[35]  M. Borodovsky,et al.  Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. , 2008, Genome research.

[36]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[37]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[38]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[39]  Steven Salzberg,et al.  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..

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

[41]  H. Vanetten,et al.  An analysis of the phylogenetic distribution of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis , 2004, Current Genetics.

[42]  L. Vaillancourt,et al.  Ultrastructural Characterization of Infection and Colonization of Maize Leaves by Colletotrichum graminicola, and by a C. graminicola Pathogenicity Mutant. , 2002, Phytopathology.

[43]  S. Covert.  Supernumerary chromosomes in filamentous fungi , 1998, Current Genetics.

[44]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[45]  H. Kistler,et al.  Mutants of Nectria haematococca created by a site-directed chromosome breakage are greatly reduced in virulence toward pea , 1996 .

[46]  R. Rodriguez,et al.  Factors Affecting the Efficient Transformation of Colletotrichum Species , 1994 .

[47]  S. Covert,et al.  A fungal gene for antibiotic resistance on a dispensable ("B") chromosome. , 1991, Science.

[48]  You-Liang Peng,et al.  A novel protein Com1 is required for normal conidium morphology and full virulence in Magnaporthe oryzae. , 2010, Molecular plant-microbe interactions : MPMI.

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