Fig. 2

Neighbor-joining tree based on 552 bp of the mitochondrial cox-1 gene. In total, 136 Strongyloides stercoralis worms from Iran are represented. For comparison, published sequences are included. Each haplotype is included in the tree only once, except for the one case where a haplotype (LC772967) was identical to a previously reported haplotype (KX226374 [14]). To the right, the nuclear SSU HVR-I haplotypes (nomenclature according to [14, 32] that were present among the bearers of the particular cox-1 haplotype are indicated, if known. Values in parentheses indicate the number of worms with this haplotype (note that the SSU HVR-I haplotype is not known for all the worms for which the cox-1 sequence was determined). Results from this study are in red. For these also, the patients with worms with this haplotype and the worms selected for whole-genome sequencing are indicated. Patients with worms of more than one cox-1 sequence are circled. The blue brackets show clusters. The two dog clusters are from [14]. Scale bar denotes 0.01 changes per nucleotide site. *Note that SSU HVR-I haplotypes II and III differ by only one nucleotide (TTT in haplotype II and TAT in haplotype III). Distinguishing homozygous III and heterozygous II/III is therefore not obvious. All three whole-genome-sequenced worms of this group turned out to be heterozygous, although only one of them had been scored as heterozygous based on the HVR-I sequencing alone. Labels: Samples starting with “Nanning” are from [19], samples starting with “Haplotype” are from [14], HTB 152_7 is from [17], samples starting with “Group” are sequences from this study and were found in multiple worms (the number of worms with the particular haplotype is indicated in parentheses), and plain accession numbers are from this study and were found in only one worm