Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations.
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.
Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.|Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.
Qi
Q
Yang
Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.|Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.
Christopher M M
CM
Franco
Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.|Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.|SARDI Aquatic Sciences, 2 Hamra Ave, West Beach, SA 5024, Australia.
Shirley J
SJ
Sorokin
Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.|Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.|Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
Wei
W
Zhang
D000818:Animals; D001483:Base Sequence; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D030541:Databases, Genetic; D056426:Genetic Loci; D005819:Genetic Markers; D010802:Phylogeny; D011161:Porifera / Q000145:classification* / Q000235:genetics*; D015203:Reproducibility of Results; D013045:Species Specificity
D005819:Genetic Markers