A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen

Ploetz, R. C. Fusarium wilt of banana. Phytopathology 105, 1512–1521, https://doi.org/10.1094/phyto-04-15-0101-rvw (2015).Article 
PubMed 

Google Scholar 
Gordon, T. R. Fusarium oxysporum and the Fusarium wilt syndrome. Annual review of phytopathology 55, 23–39, https://doi.org/10.1146/annurev-phyto-080615-095919 (2017).Article 
PubMed 

Google Scholar 
Cox, K. L. Jr., Babilonia, K., Wheeler, T., He, P. & Shan, L. Return of old foes – recurrence of bacterial blight and Fusarium wilt of cotton. Current opinion in plant biology 50, 95–103, https://doi.org/10.1016/j.pbi.2019.03.012 (2019).Article 
PubMed 

Google Scholar 
Hudson, O., Fulton, J. C., Dong, A. K., Dufault, N. S. & Ali, M. E. Fusarium oxysporum f. sp. niveum molecular diagnostics past, present and future. International Journal of Molecular Sciences 22, https://doi.org/10.3390/ijms22189735 (2021).Srinivas, C. et al. Fusarium oxysporum f. sp. lycopersici causal agent of vascular wilt disease of tomato:biology to diversity- A review. Saudi journal of biological sciences 26, 1315–1324, https://doi.org/10.1016/j.sjbs.2019.06.002 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Edel-Hermann, V. & Lecomte, C. Current status of Fusarium oxysporum formae speciales and races. Phytopathology 109, 512–530, https://doi.org/10.1094/phyto-08-18-0320-rvw (2019).Article 
PubMed 

Google Scholar 
Jangir, P. et al. Secreted in xylem genes: drivers of host adaptation in Fusarium oxysporum. Frontiers in plant science 12, 628611, https://doi.org/10.3389/fpls.2021.628611 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Yu, F. et al. Genome sequence of Fusarium oxysporum f. sp. conglutinans, the etiological agent of Cabbage Fusarium Wilt. Molecular plant-microbe interactions: MPMI 34, 210–213, https://doi.org/10.1094/mpmi-08-20-0245-a (2021).Article 
PubMed 

Google Scholar 
Ayukawa, Y. et al. A pair of effectors encoded on a conditionally dispensable chromosome of Fusarium oxysporum suppress host-specific immunity. Communications biology 4, 707, https://doi.org/10.1038/s42003-021-02245-4 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Ibrahim, S. R. M., Sirwi, A., Eid, B. G., Mohamed, S. G. A. & Mohamed, G. A. Bright Side of Fusarium oxysporum: secondary metabolites bioactivities and industrial relevance in biotechnology and nanotechnology. Journal of fungi (Basel, Switzerland) 7, https://doi.org/10.3390/jof7110943 (2021).López-Díaz, C. et al. Fusaric acid contributes to virulence of Fusarium oxysporum on plant and mammalian hosts. Molecular Plant Pathology 19, 440–453, https://doi.org/10.1111/mpp.12536 (2018).Article 
PubMed 

Google Scholar 
O’Donnell, K. et al. 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. Journal of clinical microbiology 42, 5109–5120, https://doi.org/10.1128/jcm.42.11.5109-5120.2004 (2004).Article 
PubMed 
PubMed Central 

Google Scholar 
Ortoneda, M. et al. Fusarium oxysporum as a multihost model for the genetic dissection of fungal virulence in plants and mammals. Infection and immunity 72, 1760–1766, https://doi.org/10.1128/iai.72.3.1760-1766.2004 (2004).Article 
PubMed 
PubMed Central 

Google Scholar 
Thatcher, L. F., Gardiner, D. M., Kazan, K. & Manners, J. M. A highly conserved effector in Fusarium oxysporum is required for full virulence on Arabidopsis. Molecular Plant-Microbe Interactions: MPMI 25, 180–190, https://doi.org/10.1094/mpmi-08-11-0212 (2012).Article 
PubMed 

Google Scholar 
Chen, Y. C. et al. Root defense analysis against Fusarium oxysporum reveals new regulators to confer resistance. Scientific reports 4, 5584, https://doi.org/10.1038/srep05584 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Wang, L., Calabria, J., Chen, H. W. & Somssich, M. The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview. Journal of Experimental Botany 73, 6052–6067, https://doi.org/10.1093/jxb/erac263 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Fokkens, L. et al. A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem. G3 (Bethesda, Md.) 10, 3549–3555, https://doi.org/10.1534/g3.120.401375 (2020).Article 
PubMed 

Google Scholar 
Ma, L. J. et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367–373, https://doi.org/10.1038/nature08850 (2010).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Guo, L. et al. Metatranscriptomic comparison of endophytic and pathogenic Fusarium-Arabidopsis interactions reveals plant transcriptional plasticity. Molecular Plant-Microbe Interactions: MPMI 34, 1071–1083, https://doi.org/10.1094/mpmi-03-21-0063-r (2021).Article 
PubMed 

Google Scholar 
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18, 170–175, https://doi.org/10.1038/s41592-020-01056-5 (2021).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome research 30, 1291–1305, https://doi.org/10.1101/gr.263566.120 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nature biotechnology 37, 540–546, https://doi.org/10.1038/s41587-019-0072-8 (2019).Article 
PubMed 

Google Scholar 
Hu, J. et al. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology 25, 107, https://doi.org/10.1101/2023.03.09.531669 (2024).Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics (Oxford, England) 36, 2253–2255, https://doi.org/10.1093/bioinformatics/btz891 (2020).Article 
PubMed 

Google Scholar 
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell systems 3, 95–98, https://doi.org/10.1016/j.cels.2016.07.002 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science (New York, N.Y.) 356, 92–95, https://doi.org/10.1126/science.aal3327 (2017).Article 
ADS 
PubMed 

Google Scholar 
Marbouty, M. et al. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3, e03318, https://doi.org/10.7554/eLife.03318 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Cabanettes, F. & Klopp, C. D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6, e4958, https://doi.org/10.7717/peerj.4958 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Wang, B. et al. Fo47-Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent. Molecular Plant-Microbe Interactions: MPMI 33, 1108–1111, https://doi.org/10.1094/mpmi-05-20-0116-a (2020).Article 
ADS 
PubMed 

Google Scholar 
Zhou, Z. W. et al. GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations. Journal of genetics and genomics = Yi chuan xue bao 49, 1174–1176, https://doi.org/10.1016/j.jgg.2022.03.013 (2022).Article 
PubMed 

Google Scholar 
Blin, K. et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic acids research 47, W81–w87, https://doi.org/10.1093/nar/gkz310 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Houterman, P. M., Cornelissen, B. J. & Rep, M. Suppression of plant resistance gene-based immunity by a fungal effector. PLoS pathogens 4, e1000061, https://doi.org/10.1371/journal.ppat.1000061 (2008).Article 
PubMed 
PubMed Central 

Google Scholar 
Rep, M. et al. A small, cysteine-rich protein secreted by Fusarium oxysporum during colonization of xylem vessels is required for I-3-mediated resistance in tomato. Molecular microbiology 53, 1373–1383, https://doi.org/10.1111/j.1365-2958.2004.04177.x (2004).Article 
PubMed 

Google Scholar 
Houterman, P. M. et al. The effector protein Avr2 of the xylem-colonizing fungus Fusarium oxysporum activates the tomato resistance protein I-2 intracellularly. The Plant journal: for cell and molecular biology 58, 970–978, https://doi.org/10.1111/j.1365-313X.2009.03838.x (2009).Article 
PubMed 

Google Scholar 
An, B. et al. The effector SIX8 is required for virulence of Fusarium oxysporum f.sp. cubense tropical race 4 to Cavendish banana. Fungal biology 123, 423–430, https://doi.org/10.1016/j.funbio.2019.03.001 (2019).Article 
PubMed 

Google Scholar 
Redkar, A. et al. Conserved secreted effectors contribute to endophytic growth and multihost plant compatibility in a vascular wilt fungus. The Plant Cell 34, 3214–3232, https://doi.org/10.1093/plcell/koac174 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Sperschneider, J. & Dodds, P. N. EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Molecular Plant-Microbe Interactions: MPMI 35, 146–156, https://doi.org/10.1094/mpmi-08-21-0201-r (2022).Article 
PubMed 

Google Scholar 
Bendtsen, J. D., Nielsen, H., von Heijne, G. & Brunak, S. Improved prediction of signal peptides: SignalP 3.0. Journal of molecular biology 340, 783–795, https://doi.org/10.1016/j.jmb.2004.05.028 (2004).Article 
PubMed 

Google Scholar 
Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology 305, 567–580, https://doi.org/10.1006/jmbi.2000.4315 (2001).Article 
PubMed 

Google Scholar 
Allen, G. C., Flores-Vergara, M. A., Krasynanski, S., Kumar, S. & Thompson, W. F. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature protocols 1, 2320–2325, https://doi.org/10.1038/nprot.2006.384 (2006).Article 
PubMed 

Google Scholar 
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, i884–i890, https://doi.org/10.1093/bioinformatics/bty560 (2018).Article 
PubMed 

Google Scholar 
Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology 37, 907–915, https://doi.org/10.1038/s41587-019-0201-4 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England) 25, 2078–2079, https://doi.org/10.1093/bioinformatics/btp352 (2009).Article 
PubMed 

Google Scholar 
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences 117, 9451–9457, https://doi.org/10.1073/pnas.1921046117 (2020).Article 
ADS 

Google Scholar 
Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics Chapter 4, Unit 4.10, https://doi.org/10.1002/0471250953.bi0410s05 (2004).Lomsadze, A., Burns, P. D. & Borodovsky, M. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic acids research 42, e119, https://doi.org/10.1093/nar/gku557 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR genomics and bioinformatics 3, lqaa108, https://doi.org/10.1093/nargab/lqaa108 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC bioinformatics 12, 491, https://doi.org/10.1186/1471-2105-12-491 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Korf, I. Gene finding in novel genomes. BMC bioinformatics 5, 59, https://doi.org/10.1186/1471-2105-5-59 (2004).Article 
PubMed 
PubMed Central 

Google Scholar 
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (Oxford, England) 24, 637–644, https://doi.org/10.1093/bioinformatics/btn013 (2008).Article 
PubMed 

Google Scholar 
Shao, M. & Kingsford, C. Accurate assembly of transcripts through phase-preserving graph decomposition. Nature biotechnology 35, 1167–1169, https://doi.org/10.1038/nbt.4020 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29, 644–652, https://doi.org/10.1038/nbt.1883 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics (Oxford, England) 29, 2933–2935, https://doi.org/10.1093/bioinformatics/btt509 (2013).Article 
PubMed 

Google Scholar 
Chan, P. P., Lin, B. Y., Mak, A. J. & Lowe, T. M. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic acids research 49, 9077–9096, https://doi.org/10.1093/nar/gkab688 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Wang, H. This study aimed to obtain high quality genomic sequence of Fusarium oxysporum Fo5176. BioProject https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA910529 (2023).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR22746921 (2023).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR22746920 (2023).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR22746918 (2023).NCBI GenBank https://identifiers.org/ncbi/insdc.gca:GCA_030345115.1 (2023).Wang, H. Fusarium oxysporum Fo5176, whole genome sequencing project. NGDC Genome Warehouse https://ngdc.cncb.ac.cn/gwh/Assembly/64001/show (2023).Wang, H. The annotated file for Fusarium oxysporum strain Fo5176. Figshare https://doi.org/10.6084/m9.figshare.21696389 (2023).Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell systems 3, 99–101, https://doi.org/10.1016/j.cels.2015.07.012 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Camacho, C. et al. BLAST+: architecture and applications. BMC bioinformatics 10, 421, https://doi.org/10.1186/1471-2105-10-421 (2009).Article 
PubMed 
PubMed Central 

Google Scholar 
Vollger, M. R., Kerpedjiev, P., Phillippy, A. M. & Eichler, E. E. StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics (Oxford, England) 38, 2049–2051, https://doi.org/10.1093/bioinformatics/btac018 (2022).Article 
PubMed 

Google Scholar 
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 27, 573–580, https://doi.org/10.1093/nar/27.2.573 (1999).Article 
PubMed 
PubMed Central 

Google Scholar 
Robinson, J. T. et al. Integrative genomics viewer. Nature biotechnology 29, 24–26, https://doi.org/10.1038/nbt.1754 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics (Oxford, England) 37, 1639–1643, https://doi.org/10.1093/bioinformatics/btaa1016 (2021).Article 
PubMed 

Google Scholar 
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) 26, 841–842, https://doi.org/10.1093/bioinformatics/btq033 (2010).Article 
PubMed 

Google Scholar 
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular biology and evolution 38, 4647–4654, https://doi.org/10.1093/molbev/msab199 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics (Oxford, England) 23, 1061–1067, https://doi.org/10.1093/bioinformatics/btm071 (2007).Article 
PubMed 

Google Scholar 
Jain, C., Rhie, A., Hansen, N. F., Koren, S. & Phillippy, A. M. Long-read mapping to repetitive reference sequences using Winnowmap2. Nature Methods 19, 705–710, https://doi.org/10.1038/s41592-022-01457-8 (2022).Article 
PubMed 
PubMed Central 

Google Scholar