DNA Barcoding Case Studies

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Scope

The phylum Porifera (sponges) consists of about 8,000 described species, with an estimated species number of 15,000. The Sponge Barcoding Project (SBP) aims to cover all sponge taxa, from classes Demospongiae, Hexactinellida, and Calcarea, and ranging in habitat from the marine intertidal to the deep-sea, as well as freshwater. In the long term we intend to barcode 8,000 taxa, with an initial phase of 3 years focusing on 2,000 species covering all genera. This will provide a platform from which more extensive sampling can be directed. We will start with recently described type specimens curated in associated museums and supplement these with unequivocally identifiable taxa. Fresh material of such taxa will be collected by individual groups involved in the SBP and will be taxonomically identified by an expert before barcoding. Sequencing and taxonomic identification of those 2,000 initial taxa, including consumables and appropriate storage and curation of vouchers and tissues, will cost an estimated US$100,000 per year, including salaries for technical personnel. However, project participants and associated partners will provide in-kind services for the project equal to the same amount.

Purpose

Sponges are the most basal metazoans and are notoriously difficult to identify, even by taxonomic experts. However, as a group they are highly diverse, ecologically important and of significant commercial importance to the pharmaceutical and biomaterials industry. Sponge barcodes will provide a set of indispensable tools for the identification of sponge species, and will greatly aid taxonomists, ecologists, and will enhance the discovery of drug-producing species.

Background

This is the first worldwide barcoding project on any diploblast taxon, and covers the complete taxonomic range of Porifera. Several smaller pilot studies have recently been conducted independently, with various levels of resolution and success. It has been shown, for example, that frequently co-occuring, congeneric species are difficult to separate with the standard COI barcoding fragment. However, a more variable downstream fragment appears to bear adequate resolution. Therefore, a concerted effort is now timely, and warrants comprehensive, phylum-wide coverage.

Logistics

We will focus the initial phase of the SBP on appropriately identified and curated type specimens. Samples will be obtained from associated partners at the Zoological Museum in Amsterdam/Netherlands (Dr. Rob van Soest - >18,000 specimens) and from the Queensland Museum in Brisbane/Australia (Prof. John Hooper - >34,000 specimens), or from collections of SBP partners such as the Harbor Branch Oceanographic Institution (Dr. S. Pomponi - >34,000 specimens) in Florida, USA. Initial assessments of DNA quality from these collections indicate they are of an adequate standard. DNA sequencing will be carried out either by individual SBP partners (all of whom have significant prior expertise in the field and appropriate capacities), or at the DNA sequencing facility of the coordinating institution (Göttingen Centre for Biodiversity and Ecology, Germany). Sequences and associated data (voucher and taxonomic information) will be made publicly available at the project’s website (www.spongebarcoding.org) and linked to the Barcode of Life Data Systems. Due to the fact that the highly conserved COI-barcoding primers are prone to amplify sponge commensals and/or symbionts, we will optimize sponge-specific primer design. Additionally, to resolve closely related species, we will supplement the standard fragment with 440 bp of downstream sequence. The addition of an unlinked marker such as rDNA ITS is also under consideration.

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