Additional file 2 of Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.)

Additional file 2: Table S1. List of 62 common wheat BBIs in the IWGSC RefSeq v1.1 genome assembly, including five additional genes that were excluded due to the lack of a complete BBI domain. Information includes their gene position (Gene ID based on IWGSC Refseq v1.1 gene models, name based on their homoeologous relationships, chromosome locations and order), gene structure and features (number of exons and BBI domains, BBI domain evolutionary model types [36], amino acids at P1-P1` motif position, number of complete BBI domains with all required Cys residues, protein length and molecular weight), signal peptide prediction (SP prediction as signal peptide or other, prediction confidence, predicted cleavage site position, and + = present, − = absent), pseudogene prediction (T = True, F = False), and log2TPM values of expression during development and log2 fold-change TPM of biotic and abiotic stress expression datasets. Table S2. List of BBI genes in T. aestivum, Ae. tauschii, T. urartu, T. dicoccoides, and H. vulgare for which manual curation was performed. Details of the position and confidence level of the signal peptide site are included for both the original predicted sequence and the manually curated sequence. Full details of the manual curation are provided in column K, which have been corrected for the initiation codon. All curated sequences have a signal peptide prediction greater than 0.97. BBI genes with abnormal N-terminal truncation were also listed in column G. Table S3. List of six putative wheat BBIs identified in previous studies. Information includes their original and alternative gene names, corresponding protein ID in the UniProt database, e-value for HMMscan of the BBI domain, protein sequences documented in the UniPort database, complete protein sequences based on their annotation in the IWGSC RefSeq v1.1 genome assembly and citations for the studies where these proteins were originally reported. Table S4. Common wheat BBI homoeologous groups divided by chromosome. Table S5. List of BBIs identified from O. sativa, Z. mays, B. distachyon, H. vulgare, Ae. tauschii, T. urartu and T. dicoccoides. Information includes species, gene number named by order of the gene ID from the source model, alternative name and the citation for where the name was first described, gene ID, chromosome position, BBI domain type, protein length, number of BBI domains, source of genome assembly and gene ID converter from IRGSP-1.0 to MSU for rice BBIs. For BBIs without alternative names and with uncharacterized model types, we used ‘-’ symbol. Table S6. Homologous relationships of BBIs in common wheat compared to T. urartu (AA genome), Ae. tauschii (DD genome) and T. dicoccoides (AABB genomes). Orthologous genes are presented in the same row. BBIs with uncharacterized homologous relationships were placed in separate rows and labelled “ungrouped”. Table S7. List of BBIs identified in common wheat cultivars ‘Jagger’, ‘Landmark’, ‘Julius’ and ‘Mace’. Information includes their gene ID according to the 10+ wheat genome project annotation [60], chromosome and positions, and their projections in ‘Chinese Spring’ where available. BBI genes present in some cultivars but absent from ‘Chinese Spring’ were named based on the cultivar (e.g. JA means ‘Jagger’, JU means ‘Julius’) followed by their chromosome and the physical order on that chromosome based on our de novo ORF prediction. For example, JA_1D-1 refers to the first BBI gene on ‘Jagger’ chromosome 1D that is absent from the ‘Chinese Spring’ reference assembly. Table S8. List of two common wheat BBIs identified in the “Triticum 4.0” assembly of ‘Chinese Spring’, but absent from the IWGSC RefSeq v1.1 assembly. Information includes their gene name, chromosomal location, corresponding orthologous gene from the IWGSC RefSeq v1.1 assembly, gene structure and features (exon and domain numbers, model types, P1-P1` motif residues, protein length and molecular weight) and signal peptide prediction. Table S9. Functional annotation and genomic position of all genes 200 kb upstream and downstream of BBI clusters on homoeologous group 1 and 3 chromosomes. Information includes gene ID for both high and low confidence genes, their location on each chromosome, and their functional annotation and Pfam domains based on IWGSC RefSeq v1.1 gene models [55]. BBI genes identified in our study are highlighted in red and genes annotated as other trypsin inhibitors are highlighted in blue. Table S10. Number of genes sharing functional annotation terms from IWGSC RefSeq v1.1 gene models 200 kb upstream and downstream of BBI clusters on homoeologous group 1 and 3 chromosomes. The number of BBIs on each chromosome is highlighted in red. Gene number is based on descriptive annotations from gene models. Because some BBI genes identified in our study are annotated as ‘trypsin inhibitor’ in these gene models, there is a slight discrepancy between the number of BBI genes described in this table and the total number of BBIs.