Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.