TABLE OF CONTENTS SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIGURES 1 Protocol for spreading of B. glabrata chromosome ................................................................. 4 2 Karyotype of B. glabrata and ideograms of chromosomes...................................................... 5 3 Fluorescence in situ hybridization on B. glabrata chromosomes ............................................ 6 4. SNV distribution among B. glabrata genes. ............................................................................ 7 5. Distribution of genes and genes with SNVs across KEGG Orthology (KO) categories. .................. 7 6. GO term analysis of secretome. .............................................................................................. 8 7. Secretome and tissue-specific expression ............................................................................... 9 8. Tissue-specific gene expression in B. glabrata ....................................................................... 10 9. Tissue/organ-specific expression in B. glabrata .................................................................... 11 10. GPCRs identified from the B. glabrata genome .................................................................... 14 11. GPCRs clustered on LGUN_random_Scaffold39 .................................................................. 15 12. Phylogenetic tree of commensal and cloned 16S sequences and other mollicutes ................ 16 13. Genome organization of viruses associated with Biomphalaria glabrata. ............................ 17 14. Gene structure of the B. glabrata heat shock protein (HSP) families .................................... 18 15. The number of Nimbus (BgI) elements and functional domains in the genome ................... 19 16. Phylogenetic tree of the heat shock protein (HSP) families ................................................... 20 17. Pathogen-specific expression regulation of HSP70 and Nimbus in B. glabrata .................... 21 18. Proteomics recovery of GREP-related peptides ..................................................................... 22 19. Expression of GREP-like sequences ...................................................................................... 23 20. Proteomics annotation of HSP70 family proteins .................................................................. 24 21. Proteomics annotation of HSP60 family proteins .................................................................. 25 22. Proteomics annotation of HSP90 family proteins .................................................................. 26 23. TLR signaling pathway in B. glabrata ................................................................................... 27 24. FREP domain structure .......................................................................................................... 28 25. Intron-exon structures of gastropod FREP genes ................................................................... 29 26. Phylogenetic tree FREPs ........................................................................................................ 30 27. Alignment FREP sequences ................................................................................................... 31 28. B. glabrata C1q-1 amino acid alignment ............................................................................... 40 29. Phylogenetic tree Complement C3 sequences........................................................................ 41 30. Apoptotic signaling pathways in Biomphalaria. .................................................................... 42 31. Alignment of full length caspase proteins from B. glabrata .................................................. 43 32. Bcl2-family members in B. glabrata ...................................................................................... 44 33. Production and metabolism of reactive oxygen species and nitric oxide ............................... 45 34. B. glabrata assembly lacks common AMPs .......................................................................... 46 35. CpG observed/expected (o/e) ratio in coding regions. ........................................................... 47 36. LG1i_random_Scaffold7, sequence content and CpG composition ...................................... 48 37. CpG observed/expected (o/e) ratio in repetitive regions ........................................................ 49 38. Western Blots show histone modifications ............................................................................ 50 39. ClustalW alignment of amino-acid sequences of histones H3 and H4 .................................. 51 40. Secondary structures of the B. glabrata pre-miRNA sequences ........................................... 52 41. Weblogo of B. glabrata mature miRNAs .............................................................................. 53 42. Alignment of bgl-mir-100 with animal homologs. ................................................................ 54 43. Phylogenetic tree of bgl-mir-100 with animal homologs and mir-99 precursors. ................. 55 44. Alignment of the bgl-mir-1a with homologs from Bilateria .................................................. 56 1 45. Phylogenetic tree of bgl-mir-1a and homologs from Bilateria............................................... 57 46. Alignment of bgl-mir-137 with homologs from Bilateria ...................................................... 58 47. Phylogenetic tree of bgl-mir-137 and homologs from Bilateria ............................................ 59 48. Alignment of bgl-mir-216a and bgl-mir-216b with homologs from Bilateria ....................... 60 49. Phylogenetic tree of mir-216 family, bgl-mir-216a/216b, and homologs from Bilateria and mir-283 homologs .................................................................................................................. 61 50. Alignment of bgl-mir-29a, bgl-mir-29b with homologs from Bilateria ................................. 62 51. Phylogenetic tree of bgl-mir-29a and bgl-mir-29b with homologs from Bilateria and mir-285 homologs ................................................................................................................................ 63 52. Alignment of bgl-mir-2001 with homologs from Bilateria,secondary structure of mature miRNAs ................................................................................................................................. 64 53. Alignment of bgl-mir-252a and bgl-mir-252b with homologs from Bilateria, secondary structure of mature miRNAs .................................................................................................. 65 54. RNA secondary structure of the cluster bgl-mir-71/2a-1/2d/2b/2a-2 .................................... 66 55. Alignment of the bgl-mir-1175 with homologs from Protostomia ........................................ 67 56. Phylogenetic tree of bgl-mir-1175 and homologs from Protostomia ..................................... 68 57. Alignment of bgl-mir-279 with homologs from Protostomia ................................................ 69 58. Phylogenetic tree of bgl-mir-279 and homologs from Protostomia ....................................... 70 59. Alignment of bgl-mir-750 with homologs from Protostomia ................................................ 71 60. phylogenetic tree of bgl-mir-750 and homologs from Protostomia ....................................... 72 61. Alignment of bgl-mir-1990 with homologs from Lophotrochozoa and secondary structure highlighting the mature miRNAs ........................................................................................... 73 62. Alignment of bgl-mir-1992 with homologs from Lophotrochozoa and secondary structure highlighting the mature miRNAs ........................................................................................... 74 63. RNA secondary structure of the cluster bgl-mir-745a/745b .................................................. 75 64. Alignment of bgl-mir-1986 with homologs from Mollusca and secondary structure highlighting the mature miRNAs ........................................................................................... 76 65. Alignment of B. glabrata mature miRNAs with orthologs from L. gigantea ........................ 77 66. Predicted binding sites of novel microRNAs from B. glabrata. ........................................... 80 67. Precision-recall on Anolis carolinensis hold-out data ............................................................ 81 68. Characterisation of five B. glabrata neuropeptides................................................................ 82 69.Phylogenetic tree and gene structure of ovipostatins from B. glabrata .................................. 84 70. Steroidogenesis ....................................................................................................................... 85 71. ePKs of B. glabrata, S. mansoni and Homo sapiens. ............................................................. 86 72. Phylogenetic tree of the protein serine/threonine phosphatases of B. glabrata. ................... 87 73. Phylogenetic tree of the protein tyrosine phosphatases (PTPS) of B. glabrata. .................... 87 74. Phylogenetic tree of the dual specificity phosphatases (DUSPs) of B. glabrata. ................. 88 75. Four tyrosinases map to LGUN_random_Scaffold2224 ........................................................ 89 76. Ranked high-copy TE abundance..........................................................................................