Supplementary material for "Comparative transcriptional network analysis reveals ecological specialization in infant-associated species of Bifidobacterium"

Supplementary figures, tables and legends accompanying the article "Comparative transcriptional network analysis reveals ecological specialization in infant-associated species of Bifidobacterium" (Melis-Arcos F, Arita M, Garrido D; mSystems, 2026). The study integrates pangenome analysis with transcription factor binding site (TFBS) inference and network analysis to compare regulatory architectures across Bifidobacterium longum subsp. infantis (58 genomes), B. breve (88 genomes) and B. longum subsp. longum (158 genomes). SUPPLEMENTARY FIGURES (TIFF, 300 dpi)Figure S1: Pangenome accumulation curves with power-law (Heaps' law) fits for the three species (10 genome-order permutations computed by Roary).Figure S2: Pearson correlation between predicted TFBS motifs and RegPrecise reference motifs.Figure S3: Configurational null model, with Z-scores for community counts in observed networks versus degree-preserving rewired networks.Figure S4: Rarefaction of B. longum to 58 genomes, with five network metrics at six percentile thresholds.Figure S5: Pangenome and core gene counts under rarefaction (10 subsamples of 58 genomes). SUPPLEMENTARY TABLES Table S1 (CSV): Genome metadata and assembly quality metrics (contigs, length, GC, N50/N90, L50/L90) for the 304 genomes retained after quality filtering.Table S2 (XLSX): Roary pangenome gene presence-absence matrices, one sheet per species.Table S3 (CSV): Transcription factor motif profiles analyzed in each species, with regulator family and annotated function.Table S4 (CSV): Predicted TF-target gene network edges for all three species (motif, target ortholog group, COG category, PWM score, ortholog prevalence, motif position and sequence). Supplemental_Legends.docx contains the full figure and table legends. Analysis scripts, network construction code and the Gephi project file are archived separately at https://doi.org/10.5281/zenodo.21890997.