Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers.

ABSTRACT: Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin cover

SUBMITTER: Yoshitake K 

PROVIDER: S-EPMC10033627 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature