Optimizing a Protocol for Generating Genomic Data for the Invasive Spotted Lanternfly in New Jersey
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Grant: NFS
Nicolas Largotta
CoPIs:
Brenna Levine
College:
The Dorothy and George Hennings College of Science, Mathematics, and Technology
Major:
Biology
Faculty Research Advisor(s):
Brenna Levine
Abstract:
The invasive spotted lanternfly (Lycorma delicatula), introduced to the USA in 2018, has rapidly spread throughout the Mid-Atlantic and Northeastern States, and its presence represents a significant threat to agriculture. Management of this problem species will be greatly enhanced via genomic resources facilitating identification of dispersal routes and monitoring of emergent insecticide-resistant genotypes. However, existing genetic resources for the spotted lanternfly are insufficient for parsing genomic variation. Here, we optimized a protocol for generating genomic data for the spotted lanternfly via a double-digest restrictions site associated DNA sequencing (ddRADseq) library preparation. To do so, we tested three components of the ddRADseq protocol including DNA incubation time, restriction digest incubation time, and PCR primer concentration. We identified optimal conditions by quantifying DNA concentrations, performing gel electrophoresis, and comparing pre- and post-PCR library concentrations. We found that a 48-hour DNA extraction incubation period produced adequate concentrations for sequencing while also minimizing DNA degradation. Further, we identified 6 hours as the optimal length for restriction digest incubation when using enzymes NLaIII and MLuCI to prevent over-digestion of samples. Finally, we found the optimal primer concentration for PCR to be 10 uM. This optimized protocol is currently being used for generation of large-scale genomic data for spotted lanternflies in the USA, China, and Japan.