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Using molecular systematics to enhance diagnostics and predict biosecurity risk

This five-year project ended in mid-2022.

Project Abstract

This project aimed to provide the basic taxonomic and DNA sequence data needed by MPI to deliver more effective biosecurity risk decisions. These data is needed to address the most basic questions asked when addressing biosecurity risk of an organism: what is it called? does it already occur in NZ? is it native or exotic? and, what is its lifestyle (pest/pathogen etc)?

The DNA data are essential for identification of larval life stages of most invertebrates (the life stage commonly detected in biosecurity investigations) and for the identification of currently accepted but morphologically cryptic species in many economically and environmentally important groups of fungal plant pathogens. More pragmatically, DNA sequencing is the go-to method at MPI diagnostics labs, meaning that a set of reliable DNA sequences for and accurately identified taxa of interest is central to New Zealand’s biosecurity system.

This project addressed the problem of inaccurate DNA sequence data by linking the data generated back to authentically identified specimens in NZ Arthropod Collection and the NZ Fungarium (PDD) and living cultures in ICMP. The BOLD checklist function was used to identify taxonomic gaps in DNA sequence coverage. The Manaaki Whenua specimen databases provided direct hyperlinks between the specimens sequenced and the data depositories (BOLD for arthropods, GenBank for fungi and bacteria).

Over the course of the project over 1200 arthropod species in key families of Hemiptera, Coleoptera, Lepidoptera, Hymenoptera and Diptera have been sequenced and specimens sequenced in PDD and ICMP have doubled to more than 8000, including key genera such as Phoma, Alternaria, Fusarium and Verticillium.

Integral to the project has been developing high throughput methods for more efficient sequencing and for obtaining sequences from difficult to handle material (e.g., old specimens important as early records of a pest or pathogen), and pipelines to make more effective use of sequences generated as part of the routine diagnostics in the MPI labs. Data generated through the project are now routinely included in protocols for assessment of biosecurity risk by MPI.

Biosecurity outcome

Biosecurity risk is better estimated because MPI has access to a greater range of high quality reliable reference DNA sequences derived from authentically identified specimens

Science outcome

A customised work-flow platform to produce sequences for authentically identified specimens & upload to publically accessible DNA databases (Genbank) will enhance biosecurity relevant diagnostic tool development as well as production of phylogenies that may for example, contribute to taxonomic clarification and tests of indigenous vs exotic membership

For more information and publications on this and other B3 projects, visit Zotero.

The Zotero database can be found on the B3 homepage under ‘Outputs’.