Mr Peiyuan Ye1, Dr Jinping Cheng1
1The Education University of Hong Kong, Tai Po, Hong Kong
Biography:
Peiyuan Ye is a PhD student in the Department of Science and Environmental Studies at The Education University of Hong Kong. His research focuses on environmental DNA applications in mangrove and coastal ecosystems, particularly the integration of multiple genetic markers and taxonomic groups for biodiversity assessment and biomonitoring. His current work also explores the development of regional multi-marker reference databases to improve the interpretation of marine eDNA data.
Abstract:
Regional DNA reference resources for marine invertebrate eDNA metabarcoding are often incomplete and rarely integrate multiple genetic markers. Using Hong Kong as a case study, we developed the Hong Kong Marine Invertebrate Reference Database (HKMIRD) as a framework for constructing and evaluating regional multi-marker DNA reference databases for marine invertebrate biomonitoring.
A standardized checklist of 3,413 marine invertebrate species was linked to curated reference sequences from GenBank, BOLD Systems, MIDORI, and SILVA. HKMIRD comprises marker-specific reference libraries for COI, mitochondrial 16S rRNA, and nuclear 18S rRNA. Together, these libraries contain 20,675 records and represent 2,192 species, equivalent to 64.2% of the regional fauna. The COI library had the broadest individual coverage, representing 2,042 species. When integrated after COI, the 16S rRNA and 18S rRNA libraries added references for 95 and 55 additional species, respectively, demonstrating complementary contributions to overall coverage.
Reference coverage was evaluated across markers and taxonomic groups, and HKMIRD was applied to independent coastal-water eDNA datasets generated using COI- and 18S rRNA-targeted assays. The two assays produced partly distinct taxonomic assignment profiles, showing how a multi-marker framework can integrate complementary information from different assays.
By combining a standardized regional checklist, multiple marker-specific libraries, and empirical evaluation, HKMIRD provides a practical approach for improving reference coverage and regional interpretation of marine invertebrate eDNA data. It serves as both a regional resource and a transferable framework for multi-marker eDNA biomonitoring in other coastal regions.