Dr Aimee Van Der Reis1, Emeritus Professor Lynnath Beckley2, Dr M. Pilar Olivar3, Professor Andrew Jeffs1
1University Of Auckland, , New Zealand, 2Murdoch University, Perth, Australia, 3Institut de Ciències del Mar – CSIC, Barcelona, Spain
Dietary and predator-prey studies are more frequently relying on DNA metabarcoding methods, typically achieving results that have a finer taxonomic resolution (e.g., species-level) than previous methods. With the continuous advancement in sequencing technology, what was accessible only as a large, fixed structure in a laboratory that had a limited number of users, has now advanced to a small and readily usable device. In this study, we use the gut from transformation stage lanternfish (Hygophum) specimens to compare the short-read sequencing capability of the portable Nanopore MinION and compare it to the Illumina MiSeq. Primers common in dietary DNA metabarcoding work (COI ‘Leray’ and 18S rRNA V4 ‘Zhan’) were used, with an additional comparison of cost-effective COI ‘Lobo’ primers (targeting the same COI fragment) for the proficiency in broad-range species detection. Our results indicate high congruency between sequencing machines for not only taxonomic assignments but also relative read abundance of the main dietary items. We also identified that Nanopore sequencing is more cost-effective. The Lobo primers are comparable to that of Leray, but substantially reduce the primer set price without compromising taxa detection. Using both COI and 18S broadened the taxonomic scope, providing greater prey detection. The Hygophum diet detected here aligns with previous research that suggests the main dietary items to be calanoid copepods, but using molecular methods soft prey were more readily identified compared to studies using visual methods of identification of dietary items. Overall, this study finds that Nanopore sequencing is suitable for short-read DNA metabarcoding.
Biography:
Aimee van der Reis is marine scientist and her research mainly focuses on using molecular tools to answer ecological questions. Her current work incorporates DNA metabarcoding to investigate the diet of various species for aquaculture and conservation purposes, which has included deep-sea lobsters, seabirds and fish