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References from Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus. Local targets link to admitted publications; unresolved targets remain external evidence.
Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
10.1016/j.cell.2020.05.021 · 2020 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Chestnut Blight: The Classical Problem of an Introduced Pathogen
10.2307/3807741 · 1987 · External reference
hybridSPAdes: an algorithm for hybrid assembly of short and long reads
10.1093/bioinformatics/btv688 · 2015 · External reference
SignalP 5.0 improves signal peptide predictions using deep neural networks
10.1038/s41587-019-0036-z · 2019 · External reference
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
10.1186/s12915-020-0744-3 · 2020 · External reference
Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae
10.1534/genetics.115.177709 · 2015 · External reference
Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates
10.1111/mec.13976 · 2017 · External reference
Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach
10.1109/tcbb.2018.2875479 · 2020 · External reference
Biologically Active Secondary Metabolites from the Fungi
10.1128/microbiolspec.funk-0009-2016 · 2016 · External reference
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
10.1093/nar/gkz310 · 2019 · External reference
Plant-Parasite Coevolution: Bridging the Gap between Genetics and Ecology
10.1146/annurev-phyto-072910-095301 · 2011 · External reference
Scaffolding and completing genome assemblies in real-time with nanopore sequencing
10.1038/ncomms14515 · 2017 · External reference
Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats
10.1186/s12864-015-2158-0 · 2015 · External reference
Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
10.1371/journal.pgen.1006108 · 2016 · External reference
Dynamic Large-Scale Chromosomal Rearrangements Fuel Rapid Adaptation in Yeast Populations
10.1371/journal.pgen.1003232 · 2013 · External reference
Multiple recent horizontal transfers of a large genomic region in cheese making fungi
10.1038/ncomms3876 · 2014 · External reference
Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species
10.1371/journal.ppat.1002147 · 2011 · External reference
Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes
10.1016/j.fgb.2010.09.002 · 2011 · External reference
Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods
10.1093/gigascience/giaa099 · 2020 · External reference
The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen
10.1534/genetics.115.180968 · 2015 · External reference
Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen
10.1094/phyto-12-19-0478-a · 2020 · External reference
Transposable Elements in Filamentous Fungi
10.1146/annurev.micro.57.030502.091029 · 2003 · External reference
Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe
10.1016/j.fgb.2019.06.002 · 2019 · External reference
Assessing the Phytosanitary Risk Posed by an Intraspecific Invasion of Cryphonectria parasitica in Europe
10.1094/phyto-06-19-0197-r · 2019 · External reference
Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen
10.1073/pnas.1424293112 · 2015 · External reference
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
10.1093/nar/gkz833 · 2019 · External reference
The two-speed genomes of filamentous pathogens: waltz with plants
10.1016/j.gde.2015.09.001 · 2015 · External reference
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae
10.1073/pnas.242624799 · 2002 · External reference
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
10.1073/pnas.1019315108 · 2011 · External reference
Multiple introductions of divergent genetic lineages in an invasive fungal pathogen, Cryphonectria parasitica, in France
10.1038/hdy.2009.164 · 2009 · External reference
The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen
10.1111/j.1365-294x.2012.05575.x · 2012 · External reference
A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi
10.1093/gbe/evw026 · 2016 · External reference
OrthoFinder: phylogenetic orthology inference for comparative genomics
10.1186/s13059-019-1832-y · 2019 · External reference
Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments
10.1007/978-1-0716-0199-0_14 · 2020 · External reference
Cytological and electrophoretic karyotyping of the chestnut blight fungus Cryphonectria parasitica
10.1016/j.fgb.2009.01.005 · 2009 · External reference
Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
10.1101/gr.204974.116 · 2016 · External reference
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
10.1371/journal.pgen.1000046 · 2008 · External reference
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
10.1186/gb-2011-12-1-r1 · 2011 · External reference
Considering Transposable Element Diversification in De Novo Annotation Approaches
10.1371/journal.pone.0016526 · 2011 · External reference
Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
10.1186/s12864-018-4750-6 · 2018 · External reference
The need for speed: compartmentalized genome evolution in filamentous phytopathogens
10.1111/mpp.12738 · 2019 · External reference
A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa
10.1073/pnas.132212899 · 2002 · External reference
The population biology of fungal invasions
10.1111/mec.13028 · 2015 · External reference
High-throughput functional annotation and data mining with the Blast2GO suite
10.1093/nar/gkn176 · 2008 · External reference
Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans
10.1111/j.1365-2958.2006.05076.x · 2006 · External reference
Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens
10.1186/1471-2164-15-891 · 2014 · External reference
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
10.1109/tcbb.2013.68 · 2013 · External reference
CoLoRMap: Correcting Long Reads by Mapping short reads
10.1093/bioinformatics/btw463 · 2016 · External reference
A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi
10.1186/gb-2011-12-5-r45 · 2011 · External reference
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
10.1038/ismej.2016.196 · 2017 · External reference
Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure
10.1093/gbe/evy089 · 2018 · External reference
PASTEC: An Automatic Transposable Element Classification Tool
10.1371/journal.pone.0091929 · 2014 · External reference
Genetic structure of newly established populations of Cryphonectria parasitica
10.1017/s0953756299002397 · 2000 · External reference
Whole-Genome Annotation with BRAKER
10.1007/978-1-4939-9173-0_5 · 2019 · External reference
Chromosomal Rearrangements as a Major Mechanism in the Onset of Reproductive Isolation in Saccharomyces cerevisiae
10.1016/j.cub.2014.03.063 · 2014 · External reference
Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context
10.1046/j.1365-2958.2002.03101.x · 2002 · External reference
InterProScan 5: genome-scale protein function classification
10.1093/bioinformatics/btu031 · 2014 · External reference
Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
10.1101/gr.152660.112 · 2013 · External reference
A Catalogue of the Effector Secretome of Plant Pathogenic Oomycetes
10.1146/annurev.phyto.44.070505.143436 · 2006 · External reference
New Modes of Genetic Change in Filamentous Fungi
10.1146/annurev.py.30.090192.001023 · 1992 · External reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
High‐resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two‐speed genome evolution
10.1111/mpp.12524 · 2018 · External reference
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
10.1093/bioinformatics/btw152 · 2016 · External reference
Minimap2: pairwise alignment for nucleotide sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Crypt1, an active Ac-like transposon from the chestnut blight fungus, Cryphonectria parasitica
10.1007/s004380100470 · 2001 · External reference
Evidence for interspecies transmission of viruses in natural populations of filamentous fungi in the genus Cryphonectria
10.1046/j.1365-294x.2003.01847.x · 2003 · External reference
Mechanisms and metabolomics of the host-pathogen interactions between Chestnut (Castanea species) and Chestnut blight (Cryphonectria parasitica)
10.1111/efp.12562 · 2019 · External reference
Oxford Nanopore MinION Sequencing and Genome Assembly
10.1016/j.gpb.2016.05.004 · 2016 · External reference
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
10.1038/nature08850 · 2010 · External reference
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
10.1093/bioinformatics/btw663 · 2016 · External reference
MUMmer4: A fast and versatile genome alignment system
10.1371/journal.pcbi.1005944 · 2018 · External reference
A Methylated Neurospora 5S rRNA Pseudogene Contains a Transposable Element Inactivated by Repeat-Induced Point Mutation
10.1093/genetics/149.4.1787 · 1998 · External reference
Graph analysis of fragmented long-read bacterial genome assemblies
10.1093/bioinformatics/btz219 · 2019 · External reference
Analysis of Mating-Type Genes in the Chestnut Blight Fungus, Cryphonectria parasitica
10.1006/fgbi.2001.1295 · 2001 · External reference
DNA fingerprinting and analysis of population structure in the chestnut blight fungus, Cryphonectria parasitica.
10.1093/genetics/131.2.297 · 1992 · External reference
Intercontinental Population Structure of the Chestnut Blight Fungus, Cryphonectria parasitica
10.2307/3760921 · 1996 · External reference
Recombination between Clonal Lineages of the Asexual Fungus Verticillium dahliae Detected by Genotyping by Sequencing
10.1371/journal.pone.0106740 · 2014 · External reference
Clonal population structure of the chestnut blight fungus in expanding ranges in southeastern Europe
10.1111/j.1365-294x.2008.03927.x · 2008 · External reference
A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissues
10.1093/nar/20.22.6115 · 1992 · External reference
LTR Retrotransposons in Fungi
10.1371/journal.pone.0029425 · 2011 · External reference
Transposable elements contribute to fungal genes and impact fungal lifestyle
10.1038/s41598-019-40965-0 · 2019 · External reference
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
10.1186/1471-2164-14-s1-s7 · 2013 · External reference
Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum
10.1186/s12864-018-5399-x · 2019 · External reference
The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat
10.1128/mbio.01231-16 · 2016 · External reference
Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome
10.1186/s12915-017-0457-4 · 2018 · External reference
The common ancestral core of vertebrate and fungal telomerase RNAs
10.1093/nar/gks980 · 2012 · External reference
Combined Evidence Annotation of Transposable Elements in Genome Sequences
10.1371/journal.pcbi.0010022 · 2005 · External reference
Genome evolution in filamentous plant pathogens: why bigger can be better
10.1038/nrmicro2790 · 2012 · External reference
Near-Complete Genome Assembly of Alternaria brassicae—A Necrotrophic Pathogen of Brassica Crops
10.1094/mpmi-03-19-0084-a · 2019 · External reference
deepTools2: a next generation web server for deep-sequencing data analysis
10.1093/nar/gkw257 · 2016 · External reference
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
10.1073/pnas.1400592111 · 2014 · External reference
The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
10.1146/annurev-phyto-080516-035303 · 2018 · External reference
Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora
10.1111/1755-0998.12938 · 2019 · External reference
Quality control and preprocessing of metagenomic datasets
10.1093/bioinformatics/btr026 · 2011 · External reference
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
10.1128/mbio.02275-17 · 2018 · External reference
Transposable Elements Direct The Coevolution between Plants and Microbes
10.1016/j.tig.2017.07.003 · 2017 · External reference
Premeiotic instability of repeated sequences in Neurospora crassa
10.1146/annurev.ge.24.120190.003051 · 1990 · External reference
Rearrangement of duplicated DNA in specialized cells of Neurospora
10.1016/0092-8674(87)90097-3 · 1987 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism
10.1126/science.1194573 · 2010 · External reference
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0
10.1111/mpp.12682 · 2018 · External reference
A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni
10.1093/gbe/evy240 · 2018 · External reference
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
10.1093/bioinformatics/btn013 · 2008 · External reference
Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria
10.1128/msphere.00737-20 · 2020 · External reference
Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
10.7554/elife.56279 · 2021 · External reference
A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems
10.1371/journal.ppat.1002893 · 2012 · External reference
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
10.1093/bib/bbs017 · 2012 · External reference
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model
10.1016/j.fbr.2020.07.001 · 2020 · External reference
Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum
10.1093/gbe/evz087 · 2019 · External reference
Link between epigenetic diversity and invasive status of south‐eastern European populations of phytopathogenic fungus Cryphonectria parasitica
10.1111/1462-2920.14742 · 2019 · External reference
Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection
10.3389/fpls.2017.00140 · 2017 · External reference
Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi
10.1111/mpp.12899 · 2020 · External reference
Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification
10.1111/mec.15066 · 2019 · External reference
A unified classification system for eukaryotic transposable elements
10.1038/nrg2165 · 2007 · External reference
Centromere scission drives chromosome shuffling and reproductive isolation
10.1073/pnas.1918659117 · 2020 · External reference
Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements
10.1186/s12864-016-2690-6 · 2016 · External reference
