Fungi from the genus Fusarium is a common pathogen that infects plants, human, and animals. In particular, some members from the Fusarium solani species complex (FSSC) were comparatively well-studied because the most impacted hosts were agriculturally important plants. In animals, fusariosis caused by FSSC was increasingly reported in domestic, captive and wild animals in recent decades. Whilst it is commonly reported as an opportunistic pathogen towards animals, most reports were only able to identify the disease causative FSSC members and describe its pathologic changes on the infected host. Sea turtle egg fusariosis (STEF) has been reported around the globe and has caused huge mortality in this endangered animal. However, little is known regarding the ecology and pathology of STEF. The establishment of hatchery is part of the conservation works to protect sea turtle eggs. Nonetheless, a particular hatchery practice – reusing sand for egg incubation for several nesting seasons – is to be suspected for inducing higher FSSC infection risk in incubating eggs. This study determined the microbial diversity and pathogen abundance of nest sand (Chapter 1) to find the association between used-nest sand and FSSC infection on eggs. Distinct microbiota and a higher relative abundance of FSSC were found in nest sand of sea turtle hatcheries that reuse the sand compared to the nesting beach and hatchery which did not reuse sand. This work emphasizes that stringency in hatchery management must be maintained for the efforts of conservation to not be in vain. Besides the field survey, this study further determines the genomic basis of pathogenicity in FSSC pathogens isolated from dead sea turtle eggs and various host types (Chapter 2). Highly contiguated assemblies of six FSSC strains were produced and compared, revealing a spectrum of conservation patterns in the FSSC chromosome which can be categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). Each chromosome type varied in structural architectures, with FC and LS chromosomes containing a significantly higher proportion of repetitive elements than core chromosomes and enriched in functions related to pathogenicity and niche expansion. These findings provide evidence that genome compartmentalisation was the outcome of multi-speed evolution amongst FSSC chromosomes, which is in contrast to the commonly recognized “two-speed” genome concept in fungal pathogens. In addition to the classification of FSSC’s genomic characteristics, several experiments were conducted to observe the infection scenarios and described the transcriptome responses of FSSC pathogens and Chinese soft-shelled turtle Pelodiscus sinensis eggs post-inoculation (Chapter 3). The experiments demonstrated that F. falciforme and F. keratoplasticum can penetrate eggshells and colonise egg inclusions, indicating FSSC are opportunistic pathogens toward eggs and identified differentially genes also associated with plant pathogenicity including the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. The outcome of this dissertation should allow the gain of fundamental knowledge regarding the pathology behind FSSC on eggs, which represents the beginning of critical steps towards the management of epidemics to reduce disease occurrences in the wild and man-managed settings. Moreover, this study establishes genomic resources and an animal model for fungal pathogens of the trans-kingdom hosts.

Ackerman, R. A. (1996). The nest environment and the embryonic development of sea turtles. In The Biology of Sea Turtles (Vol. 1, pp. 83–106). CRC Press.
Aist, J. R., & Bayles, C. J. (1991). Ultrastructural basis of mitosis in the fungus Nectria haematococca (sexual stage of Fusarium solani). Protoplasma, 161, 111–122.
Alexa, A., & Rahnenführer, J. (2019). TopGO: Enrichment Analysis for Gene Ontology. (2.36.0) [R Package].
Alexander, N. J., McCormick, S. P., & Hohn, T. M. (1999). TRI12, a trichothecene efflux pump from Fusarium sporotrichioides: Gene isolation and expression in yeast. Molecular and General Genetics MGG, 261(6), 977–984. https://doi.org/10.1007/s004380051046
Al-Hatmi, A. M. S., Meis, J. F., & de Hoog, G. S. (2016). Fusarium: Molecular Diversity and Intrinsic Drug Resistance. PLOS Pathogens, 12(4), e1005464. https://doi.org/10.1371/journal.ppat.1005464
Benson, G. (1999). Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research, 27(2), 573–580. https://doi.org/10.1093/nar/27.2.573
Berriman, M., Coghlan, A., & Tsai, I. J. (2018). Creation of a comprehensive repeat library for a newly sequenced parasitic worm genome. Protocol Exchange. https://doi.org/10.1038/protex.2018.054
Bertazzoni, S., Williams, A. H., Jones, D. A., Syme, R. A., Tan, K.-C., & Hane, J. K. (2018). Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. Molecular Plant-Microbe Interactions, 31(8), 779–788. https://doi.org/10.1094/MPMI-06-17-0135-FI
Bézy, V. S., Valverde, R. A., & Plante, C. J. (2015). Olive ridley sea turtle hatching success as a function of the microbial abundance in nest sand at Ostional, Costa Rica. PLoS ONE, 10(2). https://doi.org/10.1371/journal.pone.0118579
Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H., & Weber, T. (2021). antiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Research, 49(W1), W29–W35. https://doi.org/10.1093/nar/gkab335
Boughalleb, N., Armengol, J., & El Mahjoub, M. (2005). Detection of Races 1 and 2 of Fusarium solani f. Sp. Cucurbitae and their Distribution in Watermelon Fields in Tunisia. Journal of Phytopathology, 153(3), 162–168. https://doi.org/10.1111/j.1439-0434.2005.00947.x
Brown, T., Millar, Z., Evans, D., Pham, P. H., LePage, V., & Lumsden, J. S. (2020). Fusarium solani haplotype 12‐b and aortic and branchial arteritis in Hippocampus erectus Perry. Journal of Fish Diseases, 43(2), 301–304. https://doi.org/10.1111/jfd.13099
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2021). BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics, 3(1), 1–11. https://doi.org/10.1093/nargab/lqaa108
Cabañes, F. J., Alonso, J. M., Castellá, G., Alegre, F., Domingo, M., & Pont, S. (1997). Cutaneous hyalohyphomycosis caused by Fusarium solani in a loggerhead sea turtle (Caretta caretta L.). Journal of Clinical Microbiology, 35(12), 3343–3345.
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Molecular Biology and Evolution, 38(12), 5825–5829. https://doi.org/10.1093/molbev/msab293
Capella-Gutierrez, S., Silla-Martinez, J. M., & Gabaldon, T. (2009). trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25(15), 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Caracuel, Z., Roncero, M. I. G., Espeso, E. A., González-Verdejo, C. I., García-Maceira, F. I., & Di Pietro, A. (2003). The pH signalling transcription factor PacC controls virulence in the plant pathogen Fusarium oxysporum: PacC controls virulence in Fusarium. Molecular Microbiology, 48(3), 765–779. https://doi.org/10.1046/j.1365-2958.2003.03465.x
Chan, E. H. (2006). Marine turtles in Malaysia: On the verge of extinction? Aquatic Ecosystem Health and Management, 9(2), 175–184. https://doi.org/10.1080/14634980600701559
Chan, E. H. (2010). A 16-year record of green and hawksbill turtle nesting activity at Chagar Hutang Turtle Sanctuary, Redang Island, Malaysia. Indian Ocean Turtle Newsletter, 12, 1–5.
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560
Chouikh, Y., Volovitch, M., & Yot, P. (1979). A simple and fast electrophoretic method for elution of nucleic acids from gels. Mol Biol Rep., 5(4), 237–239.
Chung, W. C., Chen, L. W., Huang, J. H., Huang, H. C., & Chung, W. H. (2011). A new ‘forma specialis’ of Fusarium solani causing leaf yellowing of Phalaenopsis. Plant Pathology, 60(2), 244–252. https://doi.org/10.1111/j.1365-3059.2010.02376.x
Cobo-Díaz, J. F., Baroncelli, R., Le Floch, G., & Picot, A. (2019). Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks. Frontiers in Microbiology, 10, 261. https://doi.org/10.3389/fmicb.2019.00261
Coleman, J. J. (2016). The Fusarium solani species complex: Ubiquitous pathogens of agricultural importance. Molecular Plant Pathology, 17(2), 146–158. https://doi.org/10.1111/mpp.12289
Coleman, J. J., Rounsley, S. D., Rodriguez-Carres, M., Kuo, A., Wasmann, C. C., Grimwood, J., Schmutz, J., Taga, M., White, G. J., Zhou, S., Schwartz, D. C., Freitag, M., Ma, L., Danchin, E. G. J., Henrissat, B., Coutinho, P. M., Nelson, D. R., Straney, D., Napoli, C. A., … VanEtten, H. D. (2009). The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. PLoS Genetics, 5(8), e1000618. https://doi.org/10.1371/journal.pgen.1000618
Coleman, J. J., White, G. J., Rodriguez-Carres, M., & VanEtten, H. D. (2011). An ABC Transporter and a Cytochrome P450 of Nectria haematococca MPVI Are Virulence Factors on Pea and Are the Major Tolerance Mechanisms to the Phytoalexin Pisatin. Molecular Plant-Microbe Interactions, 24(3), 368–376. https://doi.org/10.1094/MPMI-09-10-0198
Crous, P. W., Schoch, C. L., Hyde, K. D., Wood, A. R., Gueidan, C., de Hoog, G. S., & Groenewald, J. Z. (2009). Phylogenetic lineages in the Capnodiales. Studies in Mycology, 64, 17–47. https://doi.org/10.3114/sim.2009.64.02
Crow, G. L., Brock, J. A., & Kaiser, S. (1995). Fusarium solani Fungal Infection of the Lateral Line Canal System in Captive Scalloped Hammerhead Sharks (Sphyma lewini) in Hawaii. Journal of Wildlife Diseases, 31(4), 562–565. https://doi.org/10.7589/0090-3558-31.4.562
Cuomo, C. A., Güldener, U., Xu, J.-R., Trail, F., Turgeon, B. G., Di Pietro, A., Walton, J. D., Ma, L.-J., Baker, S. E., Rep, M., Adam, G., Antoniw, J., Baldwin, T., Calvo, S., Chang, Y.-L., DeCaprio, D., Gale, L. R., Gnerre, S., Goswami, R. S., … Kistler, H. C. (2007). The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization. Science, 317(5843), 1400–1402. https://doi.org/10.1126/science.1143708
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome, 6(1), 226. https://doi.org/10.1186/s40168-018-0605-2
Dean, R., Van Kan, J. a. L., Pretorius, Z. A., Hammond-Kosack, K. E., Di Pietro, A., Spanu, P. D., Rudd, J. J., Dickman, M., Kahmann, R., Ellis, J., & Foster, G. D. (2012). The Top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology, 13(4), 414–430. https://doi.org/10.1111/j.1364-3703.2011.00783.x
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635
Dong, S., Raffaele, S., & Kamoun, S. (2015). The two-speed genomes of filamentous pathogens: Waltz with plants. Current Opinion in Genetics & Development, 35, 57–65. https://doi.org/10.1016/j.gde.2015.09.001
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460–2461. https://doi.org/10.1093/bioinformatics/btq461
Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10), 996–998. https://doi.org/10.1038/nmeth.2604
Edgar, R. C. (2016). SINTAX: A simple non-Bayesian taxonomy classifier for 16S and ITS sequences [Preprint]. Bioinformatics. https://doi.org/10.1101/074161
Edgar, R. C. (2018). Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ, 6, e4652. https://doi.org/10.7717/peerj.4652
Egidi, E., Delgado-Baquerizo, M., Plett, J. M., Wang, J., Eldridge, D. J., Bardgett, R. D., Maestre, F. T., & Singh, B. K. (2019). A few Ascomycota taxa dominate soil fungal communities worldwide. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-10373-z
Elad, D. (2011). Infections caused by fungi of the Scedosporium/Pseudallescheria complex in veterinary species. Veterinary Journal, 187(1), 33–41. https://doi.org/10.1016/j.tvjl.2010.05.028
Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1), 238. https://doi.org/10.1186/s13059-019-1832-y
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., Angiuoli, S., Bussey, H., Bowyer, P., Cotty, P. J., Dyer, P. S., Egan, A., Galens, K., Fraser-Liggett, C. M., Haas, B. J., … Nierman, W. C. (2008). Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus. PLOS Genetics, 4(4), e1000046. https://doi.org/10.1371/journal.pgen.1000046
Fernando, N., Hui, S. W., Tsang, C. C., Leung, S. Y., Ngan, A. H. Y., Leung, R. W. W., Groff, J. M., Lau, S. K. P., & Woo, P. C. Y. (2015). Fatal Fusarium solani species complex infections in elasmobranchs: The first case report for black spotted stingray (Taeniura melanopsila) and a literature review. Mycoses, 58(7), 422–431. https://doi.org/10.1111/myc.12342
Fisher, M. C., Henk, Daniel. A., Briggs, C. J., Brownstein, J. S., Madoff, L. C., McCraw, S. L., & Gurr, S. J. (2012). Emerging fungal threats to animal, plant and ecosystem health. Nature, 484(7393), 186–194. https://doi.org/10.1038/nature10947
Fokkens, L., Shahi, S., Connolly, L. R., Stam, R., Schmidt, S. M., Smith, K. M., Freitag, M., & Rep, M. (2018). The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events (p. 465070). bioRxiv. https://doi.org/10.1101/465070
Frick, W. F., Pollock, J. F., Hicks, A. C., Langwig, K. E., Reynolds, D. S., Turner, G. G., Butchkoski, C. M., & Kunz, T. H. (2010). An Emerging Disease Causes Regional Population Collapse of a Common North American Bat Species. Science, 329(5992), 679–682. https://doi.org/10.1126/science.1188594
Friedman, J., & Alm, E. J. (2012a). Inferring Correlation Networks from Genomic Survey Data. PLoS Computational Biology, 8(9), 1–11. https://doi.org/10.1371/journal.pcbi.1002687
Friedman, J., & Alm, E. J. (2012b). Inferring Correlation Networks from Genomic Survey Data. PLoS Computational Biology, 8(9), e1002687. https://doi.org/10.1371/journal.pcbi.1002687
García-Martín, J. M., Sarmiento-Ramírez, J. M., & Diéguez-Uribeondo, J. (2021). Beyond Sea Turtles: Fusarium keratoplasticum in Eggshells of Podocnemis unifilis, a Threatened Amazonian Freshwater Turtle. Journal of Fungi, 7(9), 742. https://doi.org/10.3390/jof7090742
Gijzen, M., & Nürnberger, T. (2006). Nep1-like proteins from plant pathogens: Recruitment and diversification of the NPP1 domain across taxa. Phytochemistry, 67(16), 1800–1807. https://doi.org/10.1016/j.phytochem.2005.12.008
Gilgado, F., Cano, J., Gené, J., & Guarro, J. (2005a). Molecular phylogeny of the Pseudallescheria boydii species complex: Proposal of two new species. Journal of Clinical Microbiology, 43(10), 4930–4942. https://doi.org/10.1128/JCM.43.10.4930-4942.2005
Gilgado, F., Cano, J., Gené, J., & Guarro, J. (2005b). Molecular Phylogeny of the Pseudallescheria boydii Species Complex: Proposal of Two New Species. Journal of Clinical Microbiology, 43(10), 4930–4942. https://doi.org/10.1128/JCM.43.10.4930-4942.2005
Hadwiger, L. A. (2008). Pea– Fusarium solani Interactions Contributions of a System Toward Understanding Disease Resistance. Phytopathology, 98(4), 372–379. https://doi.org/10.1094/PHYTO-98-4-0372
Han, Y., Liu, X., Benny, U., Kistler, H. C., & VanEtten, H. D. (2001). Genes determining pathogenicity to pea are clustered on a supernumerary chromosome in the fungal plant pathogen Nectria haematococca. The Plant Journal, 25(3), 305–314. https://doi.org/10.1046/j.1365-313x.2001.00969.x
Hewavisenthi, S., & Parmenter, C. J. (2001). Influence of Incubation Environment on the Development of the Flatback Turtle ( Natator depressus ). Copeia, 2001(3), 668–682. https://doi.org/10.1643/0045-8511(2001)001[0668:IOIEOT]2.0.CO;2
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2), 518–522. https://doi.org/10.1093/molbev/msx281
Hoff, K. J., & Stanke, M. (2018). Predicting Genes in Single Genomes with AUGUSTUS. Current Protocols in Bioinformatics, e57. https://doi.org/10.1002/cpbi.57
Hoh, D. Z., Lin, Y. F., Liu, W. A., Sidique, S. N. M., & Tsai, I. J. (2020). Nest microbiota and pathogen abundance in sea turtle hatcheries. Fungal Ecology, 47, 100964. https://doi.org/10.1016/j.funeco.2020.100964
Holt, C., & Yandell, M. (2011). MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12(1), 491. https://doi.org/10.1186/1471-2105-12-491
Homa, M., Galgóczy, L., Manikandan, P., Narendran, V., Sinka, R., Csernetics, Á., Vágvölgyi, C., Kredics, L., & Papp, T. (2018). South Indian Isolates of the Fusarium solani Species Complex From Clinical and Environmental Samples: Identification, Antifungal Susceptibilities, and Virulence. Frontiers in Microbiology, 9, 1052. https://doi.org/10.3389/fmicb.2018.01052
Honarvar, S., Spotila, J. R., & O’Connor, M. P. (2011). Microbial community structure in sand on two olive ridley arribada nesting beaches, Playa La Flor, Nicaragua and Playa Nancite, Costa Rica. Journal of Experimental Marine Biology and Ecology, 409(1–2), 339–344. https://doi.org/10.1016/j.jembe.2011.09.015
Hsu, L. H., Su, C. Y., Sun, P. L., & Chen, Y. L. (2021). Fusarium solani species complex infection in elasmobranchs: A case report for rough-tail stingray with valid antifungal therapy. Medical Mycology Case Reports, 32, 34–38. https://doi.org/10.1016/j.mmcr.2021.02.002
Huang, S., Kang, M., & Xu, A. (2017). HaploMerger2: Rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics, 33(16), 2577–2579. https://doi.org/10.1093/bioinformatics/btx220
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, L. J., von Mering, C., & Bork, P. (2019). eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47(D1), D309–D314. https://doi.org/10.1093/nar/gky1085
Hurst, C. J. (2019). Dirt and Disease: The Ecology of Soil Fungi and Plant Fungi That Are Infectious for Vertebrates. In C. J. Hurst (Ed.), Understanding Terrestrial Microbial Communities (Vol. 6, pp. 289–405). Springer International Publishing. https://doi.org/10.1007/978-3-030-10777-2_9
Ikeda, K., Park, P., & Nakayashiki, H. (2019). Cell biology in phytopathogenic fungi during host infection: Commonalities and differences. Journal of General Plant Pathology, 85(3), 163–173. https://doi.org/10.1007/s10327-019-00846-w
Irinyi, L., Lackner, M., de Hoog, G. S., & Meyer, W. (2016). DNA barcoding of fungi causing infections in humans and animals. Fungal Biology, 120(2), 125–136. https://doi.org/10.1016/j.funbio.2015.04.007
Jain, P. K., Gupta, V. K., Misra, A. K., Gaur, R., Bajpai, V., & Issar, S. (2011). Current Status of Fusarium Infection in Human and Animal. Asian Journal of Animal and Veterinary Advances, 6(3), 201–227. https://doi.org/10.3923/ajava.2011.201.227
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6), 587–589. https://doi.org/10.1038/nmeth.4285
Kano, R., Okayama, T., Hamamoto, M., Nagata, T., Ohno, K., Tsujimoto, H., Nakayama, H., Doi, K., Fujiwara, K., & Hasegawa, A. (2002). Isolation of Fusarium solani from a dog: Identication by molecular analysis. Medical Mycology, 40, 435–437.
Katoh, K., & Standley, D. M. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4), 772–780. https://doi.org/10.1093/molbev/mst010
Kolde, R. (2015). Pheatmap: Pretty Heatmaps (1.0.8) [R Package].
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540–546. https://doi.org/10.1038/s41587-019-0072-8
Kou, Y., Tan, Y. H., Ramanujam, R., & Naqvi, N. I. (2017). Structure–function analyses of the Pth11 receptor reveal an important role for CFEM motif and redox regulation in rice blast. New Phytologist, 214(1), 330–342. https://doi.org/10.1111/nph.14347
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120. https://doi.org/10.1128/AEM.01043-13
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455. https://doi.org/10.1093/bioinformatics/btz305
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004). Versatile and open software for comparing large genomes. Genome Biology, 5(2), R12.
Kusuda, S., Yasukawa, Y., Shibata, H., Saito, T., Doi, O., Ohya, Y., & Yoshizaki, N. (2013). Diversity in the Matrix Structure of Eggshells in the Testudines (Reptilia). Zoological Science, 30(5), 366–374. https://doi.org/10.2108/zsj.30.366
Lee, B. N., Kroken, S., Chou, D. Y. T., Robbertse, B., Yoder, O. C., & Turgeon, B. G. (2005). Functional Analysis of All Nonribosomal Peptide Synthetases in Cochliobolus heterostrophus Reveals a Factor, NPS6, Involved in Virulence and Resistance to Oxidative Stress. Eukaryotic Cell, 4(3), 545–555. https://doi.org/10.1128/EC.4.3.545-555.2005
Leslie, J. F., & Summerell, B. A. (2006). The fusarium laboratory manual (1st ed). Blackwell Pub.
Li, S., Tam, Y. K., & Hartman, G. L. (2000). Molecular Differentiation of Fusarium solani f. Sp. Glycines from Other F. solani Based on Mitochondrial Small Subunit rDNA Sequences. Phytopathology®, 90(5), 491–497. https://doi.org/10.1094/PHYTO.2000.90.5.491
Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930. https://doi.org/10.1093/bioinformatics/btt656
Limpus, C. J., Baker, V., & Miller, J. D. (1979). Movement Induced Mortality of Loggerhead Eggs. 35, 335–338.
Lindner, D. L., Gargas, A., Lorch, J. M., Banik, M. T., Glaeser, J., Kunz, T. H., & Blehert, D. S. (2011). DNA-based detection of the fungal pathogen Geomyces destructans in soils from bat hibernacula. Mycologia, 103(2), 241–246. https://doi.org/10.3852/10-262
Ling, J., Zeng, F., Cao, Y., Zhang, J., Chen, G., Mao, Z., Yang, Y., & Xie, B. (2015). Identification of a class of CFEM proteins containing a new conserved motif in Fusarium oxysporum. Physiological and Molecular Plant Pathology, 89, 41–48. https://doi.org/10.1016/j.pmpp.2014.12.001
Liu, S., Wu, B., Yang, J., Bi, F., Dong, T., Yang, Q., Hu, C., Xiang, D., Chen, H., Huang, H., Shao, C., Chen, Y., Yi, G., Li, C., & Guo, X. (2019). A Cerato-Platanin Family Protein FocCP1 Is Essential for the Penetration and Virulence of Fusarium oxysporum f. Sp. Cubense Tropical Race 4. International Journal of Molecular Sciences, 20(15), 3785. https://doi.org/10.3390/ijms20153785
Liu, Y. J., Whelen, S., & Hall, B. D. (1999). Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerase II subunit. Molecular Biology and Evolution, 16(12), 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8
Ma, L.-J., Geiser, D. M., Proctor, R. H., Rooney, A. P., O’Donnell, K., Trail, F., Gardiner, D. M., Manners, J. M., & Kazan, K. (2013). Fusarium Pathogenomics. Annual Review of Microbiology, 67(1), 399–416. https://doi.org/10.1146/annurev-micro-092412-155650
Ma, L.-J., van der Does, H. C., Borkovich, K. A., Coleman, J. J., Daboussi, M.-J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., Houterman, P. M., Kang, S., Shim, W.-B., Woloshuk, C., Xie, X., Xu, J.-R., Antoniw, J., Baker, S. E., Bluhm, B. H., … Rep, M. (2010). Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 464(7287), 367–373. https://doi.org/10.1038/nature08850
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021). 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(10), 4647–4654. https://doi.org/10.1093/molbev/msab199
Mayayo, E., Pujol, I., & Guarr, J. (1999). Experimental pathogenicity of four opportunist Fusariurn species in a murine model. 48, 363–366.
Mayjonade, B., Gouzy, J., Donnadieu, C., Pouilly, N., Marande, W., Callot, C., Langlade, N., & Muños, S. (2016). Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. BioTechniques, 61(4), 203–205. https://doi.org/10.2144/000114460
McGehee, M. A. (1990). Effects of Moisture on Eggs and Hatchlings of Loggerhead Sea Turtles (Caretta caretta). 9.
McMurdie, P. J., & Holmes, S. (2013). phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE, 8(4), e61217. https://doi.org/10.1371/journal.pone.0061217
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., & Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research, 49(D1), D412–D419. https://doi.org/10.1093/nar/gkaa913
Möller, M., & Stukenbrock, E. H. (2017). Evolution and genome architecture in fungal plant pathogens. Nature Reviews Microbiology, 15(12), 756–771. https://doi.org/10.1038/nrmicro.2017.76
Mortimer, J. A. (1999). Reducing threats to eggs and hatchlings: Hatcheries. IUCN/SSC Marine Turtle Specialist Group. http://catalog.hathitrust.org/api/volumes/oclc/42575621.html
Mortimer, J. A., Ahmad, Z., & Kaslan, S. (1993). The status of the hawksbill Eretmochelys imbricata and green turtle Chelonia mydas of Melaka and Negeri Sembilan. Malayan Nature Journal, 46(March), 243–253.
Nemec, S. (1987). Fusarium solani association with branch and trunk cankers on citrus weakened by cold weather in Florida. Mycopathologia, 97(3), 143–150. https://doi.org/10.1007/BF00437237
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32(1), 268–274. https://doi.org/10.1093/molbev/msu300
Niehaus, E.-M., Münsterkötter, M., Proctor, R. H., Brown, D. W., Sharon, A., Idan, Y., Oren-Young, L., Sieber, C. M., Novák, O., Pěnčík, A., Tarkowská, D., Hromadová, K., Freeman, S., Maymon, M., Elazar, M., Youssef, S. A., El-Shabrawy, E. S. M., Shalaby, A. B. A., Houterman, P., … Tudzynski, B. (2016). Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. Genome Biology and Evolution, 8(11), 3574–3599. https://doi.org/10.1093/gbe/evw259
O’Donnell, K., Sarver, B. A. J., Brandt, M., Chang, D. C., Noble-Wang, J., Park, B. J., Sutton, D. A., Benjamin, L., Lindsley, M., Padhye, A., Geiser, D. M., & Ward, T. J. (2007). Phylogenetic Diversity and Microsphere Array-Based Genotyping of Human Pathogenic Fusaria, Including Isolates from the Multistate Contact Lens-Associated U.S. Keratitis Outbreaks of 2005 and 2006. Journal of Clinical Microbiology, 45(7), 2235–2248. https://doi.org/10.1128/JCM.00533-07
O’Donnell, K., Sutton, D. A., Fothergill, A., McCarthy, D., Rinaldi, M. G., Brandt, M. E., Zhang, N., & Geiser, D. M. (2008). Molecular Phylogenetic Diversity, Multilocus Haplotype Nomenclature, and In Vitro Antifungal Resistance within the Fusarium solani Species Complex. Journal of Clinical Microbiology, 46(8), 2477–2490. https://doi.org/10.1128/JCM.02371-07
O’Donnell, K., Sutton, D. A., Wiederhold, N., Robert, V. A. R. G., Crous, P. W., & Geiser, D. M. (2016). Veterinary Fusarioses within the United States. Journal of Clinical Microbiology, 54(11), 2813–2819. https://doi.org/10.1128/JCM.01607-16
Parmenter, C. (1980). Incubation of the Eggs of the Green Sea Turtle, Chelonia Mydas, in Torres Strait, Australia: The Effect of Movement on Hatchability. Wildlife Research, 7(3), 487–491. https://doi.org/10.1071/WR9800487
Patino-Martinez, J., Marco, A., Quiñones, L., Abella, E., Abad, R. M., & Diéguez-Uribeondo, J. (2012). How do hatcheries influence embryonic development of sea turtle eggs? Experimental analysis and isolation of microorganisms in leatherback turtle eggs. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology, 317A(1), 47–54. https://doi.org/10.1002/jez.719
Pérez, A., Pedrós, B., Murgui, A., Casanova, M., López-Ribot, J. L., & Martínez, J. P. (2006). Biofilm formation by Candida albicans mutants for genes coding fungal proteins exhibiting the eight-cysteine-containing CFEM domain. FEMS Yeast Research, 6(7), 1074–1084. https://doi.org/10.1111/j.1567-1364.2006.00131.x
Phillott, A. D., & Parmenter, C. J. (2001). The distribution of failed eggs and the appearance of fungi in artificial nests of green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtles. Australian Journal of Zoology, 49(6), 713. https://doi.org/10.1071/ZO00051
Phillott, A. D., Parmenter, C. J., & Limpus, C. J. (2001). Mycoflora identified from failed Green (Chelonia mydas) and Loggerhead (Caretta caretta) sea turtle eggs at Heron Island, Australia. 4, 170–172.
Phillott, A. D., Parmenter, C. J., & Limpus, C. J. (2004). Occurrence of mycobiota in eastern Australian sea turtle nests. Memoirs of the Queensland Museum, 49, 701–703.
Phillott, A. D., Parmenter, C. J., & McKillup, S. C. (2006). Calcium Depletion of Eggshell After Fungal Invasion of Sea Turtle Eggs. Chelonian Conservation and Biology, 5(1), 146. https://doi.org/10.2744/1071-8443(2006)5[146:CDOEAF]2.0.CO;2
Porter, L. D., Pasche, J. S., Chen, W., & Harveson, R. M. (2015). Isolation, Identification, Storage, Pathogenicity Tests, Hosts, and Geographic Range of Fusarium solani f. Sp. Pisi Causing Fusarium Root Rot of Pea. Plant Health Progress, 16(3), 136–145. https://doi.org/10.1094/PHP-DG-15-0013
Pritchard, P. C. H. (1980). The Conservation of Sea Turtles: Practices and Problems. American Zoologist, 20(3), 609–617. https://doi.org/10.1093/icb/20.3.609
Raffaele, S., & Kamoun, S. (2012). Genome evolution in filamentous plant pathogens: Why bigger can be better. Nature Reviews Microbiology, 10(6), 417–430. https://doi.org/10.1038/nrmicro2790
Rambaut, A. (2018). FigTree (1.4.4) [Computer software].
Redkar, A., Gimenez Ibanez, S., Sabale, M., Zechmann, B., Solano, R., & Di Pietro, A. (2022). Marchantia polymorpha model reveals conserved infection mechanisms in the vascular wilt fungal pathogen Fusarium oxysporum. New Phytologist, 234(1), 227–241. https://doi.org/10.1111/nph.17909
Rehner, S. A., & Samuels, G. J. (1994). Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycological Research, 98(6), 625–634. https://doi.org/10.1016/S0953-7562(09)80409-7
Reisfeld, L., Sacristán, C., Canedo, P., Schwarz, B., Ewbank, A. C., Esperón, F., & Catão-Dias, J. L. (2019). Fusariosis in a Captive South American Sea Lion (Otaria flavescens): A Case Report. Mycopathologia, 184(1), 187–192. https://doi.org/10.1007/s11046-018-0270-9
Rep, M., & Kistler, H. C. (2010). The genomic organization of plant pathogenicity in Fusarium species. Current Opinion in Plant Biology, 13(4), 420–426. https://doi.org/10.1016/j.pbi.2010.04.004
Rogers, L. M., Flaishman, M. A., & Kolattukudy, P. E. (1994). Cutinase Gene Disruption in Fusarium solani f.sp. Pisi Decreases Its Virulence on Pea. 6, 935–945.
Rogers, L. M., Kim, Y. K., Guo, W., Gonzalez-Candelas, L., Li, D., & Kolattukudy, P. E. (2000). Requirement for either a host- or pectin-induced pectate lyase for infection of Pisum sativum by Nectria haematococca. Proceedings of the National Academy of Sciences, 97(17), 9813–9818. https://doi.org/10.1073/pnas.160271497
Romberg, M. K., & Davis, R. M. (2007). Host Range and Phylogeny of Fusarium solani f. Sp. Eumartii from Potato and Tomato in California. Plant Disease, 91(5), 585–592. https://doi.org/10.1094/PDIS-91-5-0585
Rosado-Rodríguez, G., & Maldonado-Ramírez, S. L. (2016). Mycelial Fungal Diversity Associated with the Leatherback Sea Turtle ( Dermochelys coriacea ) Nests from Western Puerto Rico. Chelonian Conservation and Biology, 15(2), 265–272. https://doi.org/10.2744/CCB-1217.1
Ruiz, F., Castelletto, M. L., Gang, S. S., & Hallem, E. A. (2017). Experience-dependent olfactory behaviors of the parasitic nematode Heligmosomoides polygyrus. PLOS Pathogens, 13(11), e1006709. https://doi.org/10.1371/journal.ppat.1006709
Salighehzadeh, R., Sharifiyazdi, H., Akhlaghi, M., Khalafian, M., Gholamhosseini, A., & Soltanian, S. (2019). Molecular and clinical evidence of Aeromonas hydrophila and Fusarium solani co-infection in narrow-clawed crayfish Astacus leptodactylus. Diseases of Aquatic Organisms, 132(2), 135–141. https://doi.org/10.3354/dao03309
Salter, C., O’Donnell, K., Sutton, D., Marancik, D., Knowles, S., Clauss, T., Berliner, A., & Camus, A. (2012). Dermatitis and systemic mycosis in lined seahorses Hippocampus erectus associated with a marine-adapted Fusarium solani species complex pathogen. Diseases of Aquatic Organisms, 101(1), 23–31. https://doi.org/10.3354/dao02506
Sarmiento-Ramírez, J. M., Abella, E., Martín, M. P., Tellería, M. T., López-Jurado, L. F., Marco, A., & Diéguez-Uribeondo, J. (2010). Fusarium solani is responsible for mass mortalities in nests of loggerhead sea turtle, Caretta caretta, in Boavista, Cape Verde: Fusarium solani in sea turtle. FEMS Microbiology Letters, 312(2), 192–200. https://doi.org/10.1111/j.1574-6968.2010.02116.x
Sarmiento-Ramírez, J. M., Abella-Pérez, E., Phillott, A. D., Sim, J., van West, P., Martín, M. P., Marco, A., & Diéguez-Uribeondo, J. (2014). Global Distribution of Two Fungal Pathogens Threatening Endangered Sea Turtles. PLoS ONE, 9(1), e85853. https://doi.org/10.1371/journal.pone.0085853
Sarmiento-Ramirez, J. M., Sim, J., Van West, P., & Dieguez-Uribeondo, J. (2017). Isolation of fungal pathogens from eggs of the endangered sea turtle species Chelonia mydas in Ascension Island. Journal of the Marine Biological Association of the United Kingdom, 97(4), 661–667. https://doi.org/10.1017/S0025315416001478
Schroers, H.-J., Samuels, G. J., Zhang, N., Short, D. P. G., Juba, J., & Geiser, D. M. (2016). Epitypification of Fusisporium ( Fusarium ) solani and its assignment to a common phylogenetic species in the Fusarium solani species complex. Mycologia, 108(4), 806–819. https://doi.org/10.3852/15-255
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303
Short, D. P. G., O’Donnell, K., Thrane, U., Nielsen, K. F., Zhang, N., Juba, J. H., & Geiser, D. M. (2013). Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. Nov. And F. petroliphilum stat. Nov. Fungal Genetics and Biology, 53, 59–70. https://doi.org/10.1016/j.fgb.2013.01.004
Sidique, S. N. M., Azuddin, N. F., & Joseph, J. (2017). First report of fusarium species at nesting sites of endangered sea turtles in Terengganu and Melaka, Malaysia. Malaysian Applied Biology, 46(3), 195–205.
Smyth, C. W., Sarmiento-Ramírez, J. M., Short, D. P. G., Diéguez-Uribeondo, J., O’Donnell, K., & Geiser, D. M. (2019). Unraveling the ecology and epidemiology of an emerging fungal disease, sea turtle egg fusariosis (STEF). PLOS Pathogens, 15(5), e1007682. https://doi.org/10.1371/journal.ppat.1007682
Sperschneider, J., & Dodds, P. N. (2022). EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes. Molecular Plant-Microbe Interactions, 35(2), 146–156. https://doi.org/10.1094/MPMI-08-21-0201-R
Stuart, S. N., Chanson, J. S., Cox, N. A., Young, B. E., Rodrigues, A. S. L., Fischman, D. L., & Waller, R. W. (2004). Status and Trends of Amphibian Declines and Extinctions Worldwide. Science, 306(5702), 1783–1786. https://doi.org/10.1126/science.1103538
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., Ruiz, L. V., Vasco-Palacios, A. M., Thu, P. Q., Suija, A., Smith, M. E., Sharp, C., Saluveer, E., Saitta, A., Rosas, M., Riit, T., Ratkowsky, D., Pritsch, K., Põldmaa, K., … Abarenkov, K. (2014). Global diversity and geography of soil fungi. Science, 346(6213), 1256688. https://doi.org/10.1126/science.1256688
Temporini, E., & VanEtten, H. (2002). Distribution of the pea pathogenicity ( PEP ) genes in the fungus Nectria haematococca mating population VI. Current Genetics, 41(2), 107–114. https://doi.org/10.1007/s00294-002-0279-x
Teufel, F., Armenteros, J. J. A., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, K. D., Winther, O., Brunak, S., Heijne, G. von, & Nielsen, H. (2021). SignalP 6.0 achieves signal peptide prediction across all types using protein language models. bioRxiv. https://doi.org/10.1101/2021.06.09.447770
Tokita, M., & Kuratani, S. (2001). Normal Embryonic Stages of the Chinese Softshelled Turtle Pelodiscus sinensis (Trionychidae). Zoological Science, 18(5), 705–715. https://doi.org/10.2108/zsj.18.705
Travis, L. B., Roberts, G. D., & Wilson, W. R. (1985). Clinical Significance of Pseudallescheria boydii: A Review of 10 Years’ Experience. Mayo Clinic Proceedings, 60(8), 531–537. https://doi.org/10.1016/S0025-6196(12)60571-0
Van Rooij, P., Martel, A., Haesebrouck, F., & Pasmans, F. (2015). Amphibian chytridiomycosis: A review with focus on fungus-host interactions. Veterinary Research, 46(1), 137. https://doi.org/10.1186/s13567-015-0266-0
Vega-Gutiérrez, T. A., Tirado-Ramírez, M. A., López-Urquídez, G. A., Angulo-Castro, A., Martínez-Gallardo, J. A., & López-Orona, C. A. (2019). Fusarium falciforme (FSSC 3 + 4) Causing Root and Stem Rot in Papaya (Carica papaya) in Mexico. Plant Disease, 103(10), 2681–2681. https://doi.org/10.1094/PDIS-05-19-0917-PDN
Vilgalys, R., & Hester, M. (1990). Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology, 172(8), 4238–4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
Wada, N., Kawamoto, T., Sato, Y., & Mano, N. (2016). A novel application of a cryosectioning technique to undecalcified coral specimens. Marine Biology, 163, 117. https://doi.org/10.1007/s00227-016-2895-x
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., & Earl, A. M. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9(11), e112963. https://doi.org/10.1371/journal.pone.0112963
Walther, G., Stasch, S., Kaerger, K., Hamprecht, A., Roth, M., Cornely, O. A., Geerling, G., Mackenzie, C. R., Kurzai, O., & von Lilienfeld-Toal, M. (2017). Fusarium Keratitis in Germany. Journal of Clinical Microbiology, 55(10), 2983–2995. https://doi.org/10.1128/JCM.00649-17
Wang, Z., Pascual-Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., Li, C., White, S., Xiong, Z., Fang, D., Wang, B., Ming, Y., Chen, Y., Zheng, Y., Kuraku, S., Pignatelli, M., Herrero, J., Beal, K., Nozawa, M., … Irie, N. (2013). The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics, 45(6), 701–706. https://doi.org/10.1038/ng.2615
Wasmann, C. C., & VanEtten, H. D. (1996). Transformation-mediated chromosome loss and disruption of a gene for pisatin demethylase decrease the virulence of Nectria haematococca on pea. Molecular Plant-Microbe Interactions, 9(9), 793–803. https://doi.org/10.1094/MPMI-9-0793
Watts, S. C., Ritchie, S. C., Inouye, M., & Holt, K. E. (2019). FastSpar: Rapid and scalable correlation estimation for compositional data. Bioinformatics, 35(6), 1064–1066. https://doi.org/10.1093/bioinformatics/bty734
Wiemann, P., Sieber, C. M. K., von Bargen, K. W., Studt, L., Niehaus, E.-M., Espino, J. J., Huß, K., Michielse, C. B., Albermann, S., Wagner, D., Bergner, S. V., Connolly, L. R., Fischer, A., Reuter, G., Kleigrewe, K., Bald, T., Wingfield, B. D., Ophir, R., Freeman, S., … Tudzynski, B. (2013). Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites. PLoS Pathogens, 9(6), e1003475. https://doi.org/10.1371/journal.ppat.1003475
Williams, A. H., Sharma, M., Thatcher, L. F., Azam, S., Hane, J. K., Sperschneider, J., Kidd, B. N., Anderson, J. P., Ghosh, R., Garg, G., Lichtenzveig, J., Kistler, H. C., Shea, T., Young, S., Buck, S.-A. G., Kamphuis, L. G., Saxena, R., Pande, S., Ma, L.-J., … Singh, K. B. (2016). Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics, 17(1), 191. https://doi.org/10.1186/s12864-016-2486-8
Winkler, M., Kaplan, O., Vejvoda, V., Klempier, N., & Martínková, L. (2009). Biocatalytic application of nitrilases from Fusarium solani O1 and Aspergillus niger K10. Journal of Molecular Catalysis B: Enzymatic, 59(4), 243–247. https://doi.org/10.1016/j.molcatb.2008.06.012
Yang, H., Yu, H., & Ma, L. J. (2020). Accessory Chromosomes in Fusarium oxysporum. Phytopathology, 110(9), 1488–1496. https://doi.org/10.1094/PHYTO-03-20-0069-IA
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018). ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6), 153. https://doi.org/10.1186/s12859-018-2129-y
Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., & Yin, Y. (2018). dbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 46(W1), W95–W101. https://doi.org/10.1093/nar/gky418
Zhang, N., O’Donnell, K., Sutton, D. A., Nalim, F. A., Summerbell, R. C., Padhye, A. A., & Geiser, D. M. (2006a). Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. Journal of Clinical Microbiology, 44(6), 2185–2190. https://doi.org/10.1128/JCM.00120-06
Zhang, N., O’Donnell, K., Sutton, D. A., Nalim, F. A., Summerbell, R. C., Padhye, A. A., & Geiser, D. M. (2006b). Members of the Fusarium solani Species Complex That Cause Infections in Both Humans and Plants Are Common in the Environment. Journal of Clinical Microbiology, 44(6), 2186–2190. https://doi.org/10.1128/JCM.00120-06
Zhang, Y., Yang, H., Turra, D., Zhou, S., Ayhan, D. H., DeIulio, G. A., Guo, L., Broz, K., Wiederhold, N., Coleman, J. J., Donnell, K. O., Youngster, I., McAdam, A. J., Savinov, S., Shea, T., Young, S., Zeng, Q., Rep, M., Pearlman, E., … Ma, L. J. (2020). The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Communications Biology, 3(1), 50. https://doi.org/10.1038/s42003-020-0770-2