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Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum f. sp. lycopercisi 4287. Fig. S10. Syntenic dotplot between FSSC and non-FSSC species. Fig. S11. Methylation level of each chromosome in FSSC. Fig. S12. Methylation analysis of F. keratoplasticum LHS11. Fig. S13. Methylation analysis of Fusarium sp. Ph1. Fig. S14. Methylation analysis of F. vanettenii Fs6. Fig. S15. Gene density in 10 kb window per chromosome or chromosome types. Fig. S16. Host attraction assay. Fig. S17. Scanning electron microscopy images. Fig. S18. Chinese soft-shelled turtle P. sinensis egg inoculated with conidia of F. falciforme Fu3 or F. keratoplasticum Fu6. Fig. S19. Principal component analyses of pathogens’ gene expression pattern of inoculated samples. Fig. S20. Principal component analyses of pathogens’ gene expression pattern of all samples. Fig. S21. Correlation plots of log2 normalized transcript per million (TPM) of one-to-one orthologous gene of F. falciforme Fu3 and F. keratoplasticum Fu6. Fig. S22. Distribution of all differentially expressed genes of FSSC pathogens during egg inoculation experiment. Fig. S23. Gene expression pattern of the animal host P. sinensis.

Additional file 3. Extended Results and Methods.

Additional file 3. Extended Results and Methods.

Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum f. sp. lycopercisi 4287. Fig. S10. Syntenic dotplot between FSSC and non-FSSC species. Fig. S11. Methylation level of each chromosome in FSSC. Fig. S12. Methylation analysis of F. keratoplasticum LHS11. Fig. S13. Methylation analysis of Fusarium sp. Ph1. Fig. S14. Methylation analysis of F. vanettenii Fs6. Fig. S15. Gene density in 10 kb window per chromosome or chromosome types. Fig. S16. Host attraction assay. Fig. S17. Scanning electron microscopy images. Fig. S18. Chinese soft-shelled turtle P. sinensis egg inoculated with conidia of F. falciforme Fu3 or F. keratoplasticum Fu6. Fig. S19. Principal component analyses of pathogens’ gene expression pattern of inoculated samples. Fig. S20. Principal component analyses of pathogens’ gene expression pattern of all samples. Fig. S21. Correlation plots of log2 normalized transcript per million (TPM) of one-to-one orthologous gene of F. falciforme Fu3 and F. keratoplasticum Fu6. Fig. S22. Distribution of all differentially expressed genes of FSSC pathogens during egg inoculation experiment. Fig. S23. Gene expression pattern of the animal host P. sinensis.

Hatchery practices are pivotal to conservation success. In sea turtle hatchery, reusing the same sand has been a norm but remains unclear whether such approach increases the risk ofFusarium solanispecies complex (FSSC) infection causing huge mortality in sea turtle eggs worldwide. We employed 16S and ITS amplicon sequencing in 123 sand samples and isolated fungal strains from diseased eggs across seven hatcheries and neighboring beaches in Malaysia. FSSC was isolated from all sampled hatcheries whereF. solani/falciformewas the predominant species. A distinct microbial composition and higher abundance of FSSC (mean = 5.2 %) was found in all but one hatchery when compared to nesting beaches (mean = 1.3 %). Specifically, an ascomycetous fungusPseudallescheria boydiiconsistently appeared in higher abundance (mean = 11.4 %) in FSSC-infected nests and was significantly associated with lower hatching success. The hatchery that maintained the most stringent practice by changing sand every nesting season had a microbiota resembling nesting beaches as well as lowest FSSC andP. boydiiabundance. The results of current study imply the need to avoid reusing sand in sea turtle hatchery.