A

B1 10410 20 30 40 50 60 70 80 90(1)TFNQLGRVDEYSKISLIKVKSLNLSSSDFPNGEENHESTGDRQDETDGNGSSSSSSSS----------------NDPEEDEADGSSSFGGAPLSSPRPQRRKLWChMuc4 (1)---QLGRVDEHSKISLIEVKLLNLRSYVFSNDDESHEGVGDRQDETEGNGSSDSSS------------------NDPEEDEEGSLGSFGGVPLSSPGPRRKKLWChMuc4 1c/1g (1)TFNQLGRVDEHSKMSLIKLKSLNLGSSGPSNDEESLKGTGDRPDGTGCNDSSSSSSSLNNPEGDEENDPEGDEGNDPEGDEGNDPNPFAGVSLSSPRPRRRNPWCpMuc4 (1)

105 191110 120 130 140 150 160 170 180(105)GRGHKGNSPHPDSEGDEADGLGSFGGAPLSSPRPSRRKLWGRGNRGGHSHSDPESDGESTGPFGGLAPRPPSPLKTIPRKTKLRKRFChMuc4 (89)KKGPKRDSSHSNPESDEDTG--PFGGAPLSSPGPRRKKLWKKGPKRDSSHSNPES-DEDTGPFGVLPPRPPSPLRGTPRKNKLKGRFChMuc4 1c/1g (84)RYGNKGKPTHSNSESDGKLG--PFDGANLKSPRLGRRRPRGRGNQGGSSNSGSDS-GGDTSQFGDPSPRPPSPYKTTPRCSKLKGRFCpMuc4(105)

ChMuc4Muc4 IIc/IIk

CpMuc4

ChMuc4Muc4 IIc/IIk

CpMuc4

0.1

Bang8 M4 Ia FJ185009

Bang5 M4 If FJ185010

Bang9 M4 IIk FJ185008

Bang26 M4 Id FJ185007

Bang4 M4 Ib FJ185006

Bang3 M4 Ie FJ185005

Bang2 M4 Id FJ185004

Bang1 M4 If FJ185003

ChMuc4 Ia Chro.20049

CpMuc4 II cgd2 420

Bang7 M4 IIk FJ184999

India4 M4 IIc FJ185002

India3 M4 IIc FJ185001

Bang21 M4 IIk FJ184998

India1 M4 IIc FJ185000

Fig A1. Polymorphic alleles of Muc4: (A) Phylogenetic tree of nucleotide sequences (from the 107th nucleotide to the end of the coding sequence) of all Bangladesh (Bang) and Indian (India) isolates from which Muc4 sequence was obtained. gp40/15 genotype is indicated after the isolate name, and the Genbank accession number follows. ChMuc4 Ia and CpMuc4 II are the published C. hominis and C. parvum sequences, respectively, and the CryptoDB (http://cryptodb.org/cryptodb/) gene name is give for these sequences. The tree was generated using Tree View (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html) from alignments generated with ClustalW2 (http://www.ebi.ac.uk/Tools/clustalw2/index.html). Bar indicates 0.1 nucleotide substitutions per site. (B) Alignment of deduced amino acid sequences of the three Muc4 alleles, beginning at amino acid 17. Non-similar amino acids are in black type on gray, conservative substitutions are dark blue on light blue and identical sequences are red on yellow.

A

1 10410 20 30 40 50 60 70 80 90(1)MMNACFYLYIIIPLLYLTFNYQSTFSQDFSTDSLAQFSLLKLTASLGNTGSDSDGSGPDDD-PPNFKPPPPPGKKGNVGSNPDGPPVPLPRTKFPGNKPPKGPGChMuc5 (1)MMNACFYLYIIIPLLYLTFNYQSTFSQDFSSDSLAQFSVLKLTASLGNTGSDSDDSGPDDE-PPNFKPPPPPGKKGNVGPSPDGPPVPLPRTKGLGSKPPKGPGMuc5 new (1)-MNACLYLYIIIPLLYLTFNYQSTFSENFSTDSLTKFSLLKLTASLGNTGSNSNDSDPEDEGPPSFVPPPPPGKKGASGSSPDGRPVPLPRTRHLGGNPPKGLGCpMuc5 (1)--NACLYLYIIIPLLYLTFNYQSTFSENFSTDSLTKFSLLKLTASLGNTGSNSNDSDPEDEGPPSFVPPPPPEKKGASGSSPDGRPVPLPRTRHLGDNPPKGLGMuc5 1c/1g (1)

105 207110 120 130 140 150 160 170 180 190(105)KPPVPTPRLRDLDGSDGGKNPDRPLGRRGGMRGRNGGNRQDKSSS--------SSSNSGSSSSPDGPVSSGGGGKGGVITVRKSPGGPPKPPERLSSLSGLLDChMuc5(104)KPPVPTPRRKYLDGTDGGKKPDRPLGRRGGMRDRNNGNKQDSSQ------------NSGSSSSTDGPVSSGGGGNSGIITVKKPSGGPPQPPTRSSSLSSLLDMuc5 new(104)KAPVPTPRLRDLDGTDGGRKPNCPLGRRGGVRGRDNGPKKDPSQSSDSSSSSSSSSSSSSNSSPDGPVSSSGDGSSGKIIVKKPPGGPPKPPTRSSSLSSLLDCpMuc5(104)KPPVPTPRLRDLDGTDGGRKPSCPLGRRGGVRGRDNGPKKDPSQSSDSSSS--SSSSSSSNSSPDGPVSSSGDGSGGKITVKKPPGGPPKPPTRSSSLSSLLDMuc5 1c/1g(103)

BChMuc5

Muc5 newCpMuc4

Muc5 IIc/IIk

ChMuc5Muc5 new

CpMuc4Muc5 IIc/IIk

0.1

Bang3 M5 Ie FJ185022

Bang9 M5 IIk FJ185021

Bang2 M5 Id FJ185023

Bang11 M5 Ib FJ185024

Bang1 M5 If FJ185025

ChMuc5 Ia Chro.20050

Bang5 M5 If FJ185015

CpMuc5 II cgd 430

India4 M5 IIc FJ185019

India3 M5 IIc FJ185018

India2 M5 IIc FJ185017

India1 M5 IIc FJ185016

Bang21 M5 IIk FJ185020

Bang7 M5 IIk FJ185011

Bang78 M5 IIk FJ185012

Bang31 M5 Ia FJ185013

Bang4 M5 Ib FJ185014

Fig A2. Polymorphic alleles of Muc5: (A) Phylogenetic tree of nucleotide sequences (from the 9th nucleotide to the end of the coding sequence) of all Bangladesh (Bang) and Indian (India) isolates from which sequence was obtained. Samples are labeled and the tree generated as described in Fig. A1A. (B) Alignment of deduced amino acid sequences of the four Muc5 alleles (complete coding sequence). Key is the same as Fig. A1B.