PT - JOURNAL ARTICLE AU - Stephen M. J. Pollo AU - Sarah J. Reiling AU - Janneke Wit AU - Matthew L. Workentine AU - Rebecca A. Guy AU - G. William Batoff AU - Janet Yee AU - Brent R. Dixon AU - James D. Wasmuth TI - Nanopore sequencing of <em>Giardia</em> reveals widespread intra-isolate structural variation AID - 10.1101/343541 DP - 2019 Jan 01 TA - bioRxiv PG - 343541 4099 - http://biorxiv.org/content/early/2019/09/19/343541.short 4100 - http://biorxiv.org/content/early/2019/09/19/343541.full AB - Background Genomes of the parasite Giardia duodenalis are relatively small for eukaryotic genomes, yet there are only six publicly available. Difficulties in assembling the tetraploid G. duodenalis genome from short read sequencing data likely contribute to this lack of genomic information. We sequenced three isolates of G. duodenalis (AWB, BGS, and beaver) on the Oxford Nanopore Technologies MinION whose long reads have the potential to address genomic areas that are problematic for short reads.Results Using a hybrid approach that combines MinION long reads and Illumina short reads to take advantage of the continuity of the long reads and the accuracy of the short reads we generated reference quality genomes for each isolate. The genomes for two of the isolates were evaluated against the available reference genomes for comparison. The third genome for which there is no previous data was then assembled. The long reads were used to find structural variants in each isolate to examine heterozygosity. Consistent with previous findings based on SNPs, Giardia BGS was found to be considerably more heterozygous than the other isolates that are from Assemblage A. We also find an enrichment of variant-specific surface proteins in some of the structural variant regions.Conclusions Our results show that the MinION can be used to generate reference quality genomes in Giardia and further be used to identify structural variant regions that are an important source of genetic variation not previously examined in these parasites.