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References from Gap-free comparative genomics uncover virulence factors for Fusarium wilt of watermelons. Local targets link to admitted publications; unresolved targets remain external evidence.
Fusarium pathogenomics
10.1146/annurev-micro-092412-155650 · 2013 · External reference
The Top 10 fungal pathogens in molecular plant pathology
10.1111/j.1364-3703.2011.00783.x · 2012 · External reference
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
10.1038/nature08850 · 2010 · External reference
Fusarium wilt of watermelon: 120 Years of Research.
2014 · External reference
Resistance to Races 0, 1, and 2 of Fusarium wilt of watermelon in Citrullus sp. PI-296341 -FR
10.21273/hortsci.26.4.429 · 1991 · External reference
Variation in pathogenicity of Fusarium oxysporum f. sp. niveum and resistance in watermelon cultivars
1972 · External reference
Physiological races and soil population level of Fusarium wilt of watermelon
10.1007/bf02980343 · 1976 · External reference
Race 3, a new and highly virulent race of Fusarium oxysporum f. sp. niveum causing Fusarium wilt in watermelon
10.1094/pdis-94-1-0092 · 2010 · External reference
First report of Fusarium oxysporum f. sp. niveum Race 3 causing wilt of watermelon
2022 · External reference
Genetic analysis and chromosome mapping of resistance to Fusarium oxysporum f. sp. niveum (FON) race 1 and race 2 in watermelon (Citrullus lanatus L.)
10.1007/s11032-015-0375-5 · 2015 · External reference
Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding
10.1038/s41588-024-01823-6 · 2024 · External reference
First report of Fusarium oxysporum f. sp. niveum Race 3 causing wilt of watermelon in Florida, U.S.A.
10.1094/pdis-10-17-1649-pdn · 2018 · External reference
The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events
2018 · External reference
Advances and challenges in computational prediction of effectors from plant pathogenic fungi
10.1371/journal.ppat.1004806 · 2015 · External reference
Genome-wide analysis in three Fusarium pathogens identifies rapidly evolving chromosomes and genes associated with pathogenicity
10.1093/gbe/evv092 · 2015 · External reference
Effector profiles distinguish formae speciales of Fusarium oxysporum
10.1111/1462-2920.13445 · 2016 · External reference
The root-invading pathogen Fusarium oxysporum targets pattern-triggered immunity using both cytoplasmic and apoplastic effectors
10.1111/nph.16618 · 2020 · External reference
Six de novo assemblies from pathogenic and nonpathogenic strains of Fusarium oxysporum f. sp. niveum
10.1094/phytofr-04-21-0031-sc · 2022 · External reference
A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding
10.1016/j.molp.2022.06.010 · 2022 · External reference
Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin
10.1128/jcm.42.11.5109-5120.2004 · 2004 · External reference
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
10.1038/s41592-020-01056-5 · 2021 · External reference
Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments
10.1016/j.cels.2016.07.002 · 2016 · External reference
Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom
10.1016/j.cels.2015.07.012 · 2016 · External reference
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads
2020 · External reference
BUSCO: assessing genomic data quality and beyond
10.1002/cpz1.323 · 2021 · External reference
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes
10.1101/gr.6743907 · 2008 · External reference
Unresolved reference
External reference
Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent
10.1094/mpmi-05-20-0116-a · 2020 · External reference
OrthoFinder: phylogenetic orthology inference for comparative genomics
10.1186/s13059-019-1832-y · 2019 · External reference
New domain motif: the structure of pectate lyase C, a secreted plant virulence factor
10.1126/science.8502994 · 1993 · External reference
Secreted in Xylem Genes: drivers of host adaptation in Fusarium oxysporum
10.3389/fpls.2021.628611 · 2021 · External reference
Fungal effectors: past, present, and future
10.1016/j.mib.2024.102526 · 2024 · External reference
EffectorP 3.0: Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes
10.1094/mpmi-08-21-0201-r · 2022 · External reference
SignalP 5.0 improves signal peptide predictions using deep neural networks
10.1038/s41587-019-0036-z · 2019 · External reference
Unresolved reference
2022 · External reference
The Fusarium oxysporum effector Six6 contributes to virulence and suppresses I-2-mediated cell death
10.1094/mpmi-11-13-0330-r · 2014 · External reference
The FonSIX6 gene acts as an avirulence effector in the Fusarium oxysporum f. sp. niveum - watermelon pathosystem
10.1038/srep28146 · 2016 · External reference
A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-Fungal pathosystem
10.1534/g3.120.401375 · 2020 · External reference
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
10.1038/s41564-022-01287-6 · 2023 · External reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · 2022 · External reference
Formation and transfer of disulphide bonds in living cells
10.1038/nrm954 · 2002 · External reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · 2024 · External reference
A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen
10.1038/s41597-024-03763-6 · 2024 · External reference
A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis-cucumerinum
10.1111/j.1462-2920.2007.01329.x · 2007 · External reference
Fusarium oxysporum f. sp. niveum Pumilio 1 regulates virulence on watermelon through Interacting with the ARP2/3 complex and binding to an A-rich motif in the 3’ UTR of diverse transcripts. Idnurm A, editor
2023 · External reference
A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide
10.1038/nprot.2006.384 · 2006 · External reference
Hi-C: a comprehensive technique to capture the conformation of genomes
10.1016/j.ymeth.2012.05.001 · 2012 · External reference
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
10.1093/bioinformatics/btr011 · 2011 · External reference
GenomeScope: fast reference-free genome profiling from short reads
10.1093/bioinformatics/btx153 · 2017 · External reference
Minimap2: pairwise alignment for nucleotide sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
Database indexing for production MegaBLAST searches
10.1093/bioinformatics/btn322 · 2008 · External reference
Towards complete and error-free genome assemblies of all vertebrate species
10.1038/s41586-021-03451-0 · 2021 · External reference
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
10.1126/science.aal3327 · 2017 · External reference
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
10.1186/s13059-020-02134-9 · 2020 · External reference
RepeatModeler2 for automated genomic discovery of transposable element families
10.1073/pnas.1921046117 · 2020 · External reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
10.1038/s41587-019-0201-4 · 2019 · External reference
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
10.1038/nbt.3122 · 2015 · External reference
UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view
10.1007/978-1-4939-3167-5_2 · 2016 · External reference
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
2021 · External reference
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
10.1186/1471-2105-12-491 · 2011 · External reference
eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale
10.1093/molbev/msab293 · 2021 · External reference
Near-optimal probabilistic RNA-seq quantification
10.1038/nbt.3519 · 2016 · External reference
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
10.1093/nar/gkab301 · 2021 · External reference
JCVI: A versatile toolkit for comparative genomics analysis
10.1002/imt2.211 · 2024 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Complex heatmap visualization
2022 · External reference
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
10.1038/75556 · 2000 · External reference
The Gene Ontology knowledgebase in 2023
2023 · External reference
Homology-based annotation of large protein datasets.
10.1007/978-1-4939-3572-7_8 · 2016 · External reference
clusterProfiler: an R package for comparing biological themes among gene clusters
10.1089/omi.2011.0118 · 2012 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Unresolved reference
External reference
Functional analysis of the kinome of the wheat scab fungus Fusarium graminearum
10.1371/journal.ppat.1002460 · 2011 · External reference
Split-marker recombination for efficient targeted deletion of fungal genes
10.4148/1941-4765.1150 · 2003 · External reference
Deletion and allelic exchange of the Aspergillus fumigatus veA locus via a novel recyclable marker module
10.1128/ec.4.7.1298-1307.2005 · 2005 · External reference
Localisation of the benzimidazole fungicide binding site of Gibberella zeae β2-tubulin studied by site-directed mutagenesis
10.1002/ps.2050 · 2011 · External reference
Cellular localization and role of kinase activity of PMK1 in Magnaporthe grisea
10.1128/ec.3.6.1525-1532.2004 · 2004 · External reference
Efficient approaches for generating GFP fusion and epitope-tagging constructs in filamentous fungi.
10.1007/978-1-61779-040-9_15 · 2011 · External reference
The assembies and annotations of three Fusarium oxysporum (R1 R2 R3)
2025 · External reference
GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations
10.1016/j.jgg.2022.03.013 · 2022 · External reference
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · 2022 · External reference
