Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

Qi Yang,Christopher M M Franco,Shirley J Sorokin,Wei Zhang

doi:10.1038/srep41422

Qi Yang, Christopher M M Franco + Show 2 more

Open Access

https://doi.org/10.1038/srep41422

Copy DOI

Abstract

For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3–D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.

Highlights

Sponges, the evolutionary oldest multicellular animals, are sessile, benthic filter-feeders[1]
We applied DNA markers to assist in the identification of individuals against already known species, which consists of comparing standardised stretches of DNA to reference databases to identify sponges
The nuclear ribosomal genes of eukaryotes, such as the 28S rRNA genes[31], are arranged in tandemly repeated clusters, where transcribed units alternate with non-transcribed units called spacers, such as the internal transcribed spacer 1 (ITS1) and 2 (ITS2)[32]

Summary

Introduction

Sponges (phylum Porifera), the evolutionary oldest multicellular animals, are sessile, benthic filter-feeders[1]. Traditional morphological identification methods often lead to erroneous classification[14,15], and the actual species diversity and distribution may be underestimated[16] Molecular approaches, such as DNA barcoding, provide a potential solution for sponge classification[17,18,19]. The COI mtDNA locus is a conservative region but with highly variable sequences It is the most commonly used mitochondrial marker of approximately 700 bp at the 5′end of the cytochrome c oxidase subunit I gene (COI locus). This gene is relatively easy to amplify as it is conserved across multicellular animals[25] and abundant in eukaryotic DNA26. They have been used for phylogenetic and phylogeographic analyses of non-bilaterian metazoans such as corals[34] and sponges[35]

Objectives

Methods

Results

Conclusion