Additional file 9: Table S7. Differentially expressed genes in R5 that mapped to the virulence-as... more Additional file 9: Table S7. Differentially expressed genes in R5 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 8: Table S6. Differentially expressed genes in R2 that mapped to the virulence-as... more Additional file 8: Table S6. Differentially expressed genes in R2 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 6: Table S4. Differentially expressed Fop genes detected in R6 at 20 dpi - column... more Additional file 6: Table S4. Differentially expressed Fop genes detected in R6 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 7: Table S5. Differentially expressed genes in R1 that mapped to the virulence-as... more Additional file 7: Table S5. Differentially expressed genes in R1 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 5: Table S3. Differentially expressed Fop genes detected in R5 at 20 dpi - column... more Additional file 5: Table S3. Differentially expressed Fop genes detected in R5 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 17: Table S15. Number of genes encoding characterized and putative cell wall degr... more Additional file 17: Table S15. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R2 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 1: Fig. S1. Venn diagram of Fop genes differentially expressed between in vitro a... more Additional file 1: Fig. S1. Venn diagram of Fop genes differentially expressed between in vitro and in planta and upregulated in the root (R) and shoot tissues (S) at 20 dpi for the four races.
Additional file 3: Table S1. Differentially expressed Fop genes detected in R1 at 20 dpi - column... more Additional file 3: Table S1. Differentially expressed Fop genes detected in R1 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 18: Table S16. Number of genes encoding characterized and putative cell wall degr... more Additional file 18: Table S16. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R6 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 10: Table S8. Differentially expressed genes in R6 that mapped to the virulence-a... more Additional file 10: Table S8. Differentially expressed genes in R6 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 16: Table S14. Number of genes encoding characterized and putative cell wall degr... more Additional file 16: Table S14. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R5 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 15: Table S13. Number of genes encoding characterized and putative cell wall degr... more Additional file 15: Table S13. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R1 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 9: Supplementary Figure 6. Maximum likelihood consensus tree with bootstrap node ... more Additional file 9: Supplementary Figure 6. Maximum likelihood consensus tree with bootstrap node support of > 70% was inferred from the sequences of the large variable region of Variant 2 and 3 Fusarium oxysporum isolates. One reference isolate per variant type (V2-DF041, V3-NRRL37622) from Brankovics et al. [23] was included in the analysis. The trees were not rooted.
Additional file 8: Supplementary Figure 5. Maximum likelihood consensus tree with bootstrap node ... more Additional file 8: Supplementary Figure 5. Maximum likelihood consensus tree with bootstrap node support of > 70% was inferred from the sequences of the large variable region of Variant 1 Fusarium oxysporum isolates. Eight reference isolates (Foc001, NRRL25433, Fon002, Fod001, NRRL54005, F11, NRRL26381 and Forc016) from Brankovics et al. [23] were included in the analysis. The tree was rooted to Fusarium proliferatum (ITEM2287).
Additional file 7: Supplementary Figure 4. One Way ANOVA and Fisher test for Least Significant Di... more Additional file 7: Supplementary Figure 4. One Way ANOVA and Fisher test for Least Significant Difference between the length of the conserved region of different variant types present in the Fusarium oxysporum isolates used for phylogenetic analyses
Additional file 5: Supplementary Figure 2. Box and whisker plots showing the spread of Fusarium o... more Additional file 5: Supplementary Figure 2. Box and whisker plots showing the spread of Fusarium oxysporum mitochondrial genome length, length of the conserved region and large variable region.
Additional file 9: Table S7. Differentially expressed genes in R5 that mapped to the virulence-as... more Additional file 9: Table S7. Differentially expressed genes in R5 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 8: Table S6. Differentially expressed genes in R2 that mapped to the virulence-as... more Additional file 8: Table S6. Differentially expressed genes in R2 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 6: Table S4. Differentially expressed Fop genes detected in R6 at 20 dpi - column... more Additional file 6: Table S4. Differentially expressed Fop genes detected in R6 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 7: Table S5. Differentially expressed genes in R1 that mapped to the virulence-as... more Additional file 7: Table S5. Differentially expressed genes in R1 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 5: Table S3. Differentially expressed Fop genes detected in R5 at 20 dpi - column... more Additional file 5: Table S3. Differentially expressed Fop genes detected in R5 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 17: Table S15. Number of genes encoding characterized and putative cell wall degr... more Additional file 17: Table S15. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R2 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 1: Fig. S1. Venn diagram of Fop genes differentially expressed between in vitro a... more Additional file 1: Fig. S1. Venn diagram of Fop genes differentially expressed between in vitro and in planta and upregulated in the root (R) and shoot tissues (S) at 20 dpi for the four races.
Additional file 3: Table S1. Differentially expressed Fop genes detected in R1 at 20 dpi - column... more Additional file 3: Table S1. Differentially expressed Fop genes detected in R1 at 20 dpi - column 1 with other analyses such as: predicted proteins - column 2, conserved domain - column 3, log2fold change - column 4, subcellular localisation of the effector-like proteins - column 5, protein length - column 6, and GO functional enrichment for biological processes (BP) - column 7. DEGs predicted to be effector-like are shaded yellow and they were all located on the adaptive genome.
Additional file 18: Table S16. Number of genes encoding characterized and putative cell wall degr... more Additional file 18: Table S16. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R6 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 10: Table S8. Differentially expressed genes in R6 that mapped to the virulence-a... more Additional file 10: Table S8. Differentially expressed genes in R6 that mapped to the virulence-associated genes on the PHI-base database.
Additional file 16: Table S14. Number of genes encoding characterized and putative cell wall degr... more Additional file 16: Table S14. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R5 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 15: Table S13. Number of genes encoding characterized and putative cell wall degr... more Additional file 15: Table S13. Number of genes encoding characterized and putative cell wall degrading enzymes of the Fop R1 transcriptome. Note: Protein Ids are used under activities and where there was no name associated with the unigene, protein domain is provided and where there is no protein IDs and domains, HP is stated, denoting hypothetical protein with the CAZYme family associated with the amino acid sequences of the unigenes.
Additional file 9: Supplementary Figure 6. Maximum likelihood consensus tree with bootstrap node ... more Additional file 9: Supplementary Figure 6. Maximum likelihood consensus tree with bootstrap node support of > 70% was inferred from the sequences of the large variable region of Variant 2 and 3 Fusarium oxysporum isolates. One reference isolate per variant type (V2-DF041, V3-NRRL37622) from Brankovics et al. [23] was included in the analysis. The trees were not rooted.
Additional file 8: Supplementary Figure 5. Maximum likelihood consensus tree with bootstrap node ... more Additional file 8: Supplementary Figure 5. Maximum likelihood consensus tree with bootstrap node support of > 70% was inferred from the sequences of the large variable region of Variant 1 Fusarium oxysporum isolates. Eight reference isolates (Foc001, NRRL25433, Fon002, Fod001, NRRL54005, F11, NRRL26381 and Forc016) from Brankovics et al. [23] were included in the analysis. The tree was rooted to Fusarium proliferatum (ITEM2287).
Additional file 7: Supplementary Figure 4. One Way ANOVA and Fisher test for Least Significant Di... more Additional file 7: Supplementary Figure 4. One Way ANOVA and Fisher test for Least Significant Difference between the length of the conserved region of different variant types present in the Fusarium oxysporum isolates used for phylogenetic analyses
Additional file 5: Supplementary Figure 2. Box and whisker plots showing the spread of Fusarium o... more Additional file 5: Supplementary Figure 2. Box and whisker plots showing the spread of Fusarium oxysporum mitochondrial genome length, length of the conserved region and large variable region.
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