title: Sequences for two contigs removed during decontamination proccess
design: High molecular weight (HMW) genomic DNA extraction and purification from the sample was performed using the MagAttract HMW DNA Kit (Qiagen Inc., Venlo, Netherlands) as per manufacturers instructions. High molecular weight DNA was confirmed using a FemtoPulse (Advanced Analytical Technologies Inc., Ankeny, IA). The HMW DNA (10ug aliquots) were converted to SMRTbell templates using the SMRTbell prep kit 3.0 (Pacific Biosciences, Menlo Park, CA) as per manufacturers instructions. Briefly, samples were end-repaired and ligated to blunt adaptors. Exonuclease treatment was performed to remove unligated adapters and damaged DNA fragments. Samples were purified using 0.6x AMPureXP beads (Beckman Coulter Inc., Brea, CA). The purified SMRTbell librarieswere eluted in 10 l of elution buffer. Eluted SMRTbell libraries were size selected on the BluePippin (Sage Science Inc., Beverly, MA) to eliminate library fragments below approximately 10 Kbp. Final library quantification and sizing was carried out on a FemtoPulse (Advanced Analytical Technologies Inc., Ankeny, IA) using 1 l of library. The amount of primer and polymerase required for the binding reaction was determined using the SMRTbell concentration and library insert size. Primers were annealed and polymerase was bound to the SMRTbell template. Sequencing was performed using the Revio platform (Pacific Biosciences, Menlo Park, CA). The HiFi libraries were run on Revio system 25M SMRT cells using sequencing chemistry 3.0 with 4-hour pre-extension and 30-hour movie time. For decontamination, The Basic Local Alignment Search Tool (BLASTn v2.15.0+; Altschul et al. 1990; Camacho et al. 2009)  was used to query the contigs against the nt_core database v1.1 to check for contamination. Hits with an e-value cutoff of 0.01 and longer than 200 bp were examined. Contigs with only hits to insects and ribosomal RNA were not considered contamination. All other contigs represented possible contamination and were removed from the final assembly and annotation.