Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

• DOI: 10.7717/peerj.10340
• Publication Date: 2020-11-13T08:21:01Z
• Authors: Pacharaporn Angthong; Tanaporn Uengwetw...; Wirulda Pootakham; Kanchana Sittikan...; Chutima Sonthirod; Duangjai Sangsrakru; Thippawan Yoocha; Intawat Nookaew; Thidathip Wongsur...; Piroon Jenjaroenpun; Wanilada Rungrass...; Nitsara Karoonuth...
• Keywords: genomic DNA

Marine organisms are important to global food security as they the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving environment ensure sufficient and sustainable production for security. However, only few high-quality genome sequences marine organisms, especially shellfish, available public partly because difficulty in sequence assembly due complex nature their genomes. A key step a successful sequencing is preparation high molecular weight (HMW) genomic DNA. This study evaluated effectiveness five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Animals Sbeadex livestock kits) obtaining shrimp HMW long-read platform. samples were assessed quality quantity using Qubit fluorometer, NanoDrop spectrophotometer pulsed-field gel electrophoresis. Among methods examined without further optimization, Genomic-tip kit yielded with highest quality. modifications these established might even better quantity. To investigate whether obtained could be used application, from top three (CTAB method, Pacific Biosciences (PacBio) library construction sequencing. Genomic kits allowed construction, CTAB method did not. isolated higher number long reads (N50 14.57 Kb) than those 9.74 Kb). Thus, this identified an effective that applied other