title: Deep amplicon sequences of 18S rDNA HRV-IV: Strongyloides strercoralis from dog in Sydney, Australia
design: Total DNA was isolated from 200 mg of fresh faeces using ISOLATE II Fecal DNA Kit (Bioline) and eluted in 75 l and stored at -20C prior to PCR. The nuclear 18S rRNA (HVR-I and HVR-IV) and mitochondrial cox1 PCR assays were used to type the material (https://doi.org/10.1371/journal.pntd.0007609). Samples were amplified in 30 L total volume of PCR with SensiFAST SYBR No-ROX Kit (Bioline Australia) and 3 L of DNA template. All primers were adapted for Illumina sequencing. The assay was run on CFX Opus 96 Real-Time PCR System (Biorad, Australia) using the following cycle steps 95C for 3 minutes, followed by 27 cycles of 95C for 5 s, 63C for 15 s and 72C. Amplicons were submitted for amplicon deep sequencing using Illumina NGS at the Ramaciotti Centre for Genomics, University of New South Wales, Sydney, Australia and sequenced on MiSeq using MiSeq Reagent Kits v2 (250PE, Illumina).