Additional file 3: of Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

Sequences of the constructs used for the generation of ΔXT/FT. (PDF 168 kb

Additional file 4: of Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

Differential gene expression analysis results. (TXT 4526 kb

Additional file 8 of Comparative genome characterization of the periodontal pathogen Tannerella forsythia

Additional file 8: Table S8. Codon usage bias (scnRCA) including “hypothetical proteins”. Top 20 genes of ATCC 43037 (a) and Tannerella sp. BU063 (b) showing the highest scnRCA values

Additional file 2: of Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

High-throughput sequencing data. (ODS 25 kb

Additional file 5: of Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

High impact variants. (TXT 441 kb

Additional file 1: of Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

Table S1. Transposable elements within the N. benthamiana reference genome. Table S2. BUSCO analysis to assess gene set completeness. Table S3. Number of sequences, database total length of each constructed database. Table S4. Normalized counts for target genes of the FucT and XylT transgenes. Table S5. Regions of FucT1, FucT-pseudogene, XylT1, XylT2 targeted by transgenes. Table S6. Primer sequences for qPCR. Table S7. Potential off-target effects of FucT-transgene and XylT-transgene. Table S8. Pearson's correlation between normalized counts of the four mRNA-seq samples. Figure S1. Gene models obtained by mapping sequences of FucT and XylT genes onto the Nb-1 draft genome assembly. Figure S2. Genomic coverage of transgenes within the ΔXT/FT genome. Figure S3. Genomic coverage in ΔXT/FT and wild type on scaffold Niben101Scf03674 and Niben101Scf03823. Figure S4. Re-assembly of region of insertion of XylT transgene. Figure S5. Alignment between scaffolds containing genes g76921 and g54961. Figure S6. Protein sequence alignment between genes g76921 and g54961. Figure S7. Multiple sequence alignment of g76921 and g54961. Figure S8. Folding of N. benthamiana proteins encoded by g76921 and g54961. Figure S9. Principal component analysis (PCA) on normalized read counts. Figure S10. ΔΔCT values and TPM for differentially expressed genes. Figure S11. Insert size estimation of ΔXT/FT, WT genomic sequencing libraries. (PDF 8074 kb

Additional file 11 of Comparative genome characterization of the periodontal pathogen Tannerella forsythia

Additional file 11: Figure S2. Blast Score Ratio values plotted as heatmap for 45 suggested virulence genes in ten T. forsythia strains and the genome of a putative health-associated Tannerella sp. BU063. In contrast to Fig. 4, the 45 gene sequences were blasted against sequences of annotated CDS in each genome

Additional file 7 of Comparative genome characterization of the periodontal pathogen Tannerella forsythia

Additional file 7: Table S7. Codon usage bias (scCAI) including “hypothetical proteins”. Top 20 genes of ATCC 43037 (a) and Tannerella sp. BU063 (b) showing the highest scCAI values

Additional file 6 of Comparative genome characterization of the periodontal pathogen Tannerella forsythia

Additional file 6: Table S6. Codon usage bias (scnRCA). Top 20 genes of ATCC 43037 (a) and Tannerella sp. BU063 (b) showing the highest scnRCA values. Only functionally annotated proteins were selected

Additional file 10 of Comparative genome characterization of the periodontal pathogen Tannerella forsythia

Additional file 10: Figure S1. Span size distribution of the mate-pair library prepared from DNA of T. forsythia strain ATCC 43037. The peak of the distribution is at 1759 bp, indicated by the red line