Organisms Diversity & Evolution

, Volume 16, Issue 1, pp 53–64 | Cite as

A short LSU rRNA fragment as a standard marker for integrative taxonomy in calcareous sponges (Porifera: Calcarea)

  • Oliver VoigtEmail author
  • Gert Wörheide
Original Article


Calcareous sponges are taxonomically difficult, and their morpho-systematic classification often conflicts with molecular phylogenies. Consequently, species descriptions that rely solely on morphological characters,and taxonomic revisions appear to provide little to no information about phylogenetic affiliations and integrative approaches, combining DNA and morphological data, are applied more frequently. However, a standardized database that combines DNA sequence and morphological specimen information is still missing for calcareous sponges. The mitochondrial cytochrome oxidase subunit 1 gene (COI) is the marker of choice for rapid species identification in many other animal taxa, including demosponges, for which COI sequences and morphological information have been compiled in the sponge barcoding database ( But due to the peculiarities of calcarean mitochondrial genomes, sequencing COI in Calcarea is methodologically challenging. We here propose the use of one more commonly used DNA marker, the C-region of the 28S gene (LSU), as standard barcoding marker for Calcarea, after also considering the internal transcribed spacer (ITS) region for such proposes. Especially in the subclass Calcaronea, we observed severe problems of high intra- and intergenomic variation that impedes pan-calcarean ITS alignments. In contrast, the C-region of LSU provides a short but phylogenetically informative DNA sequence, alignable across both subclasses with the help of a newly developed secondary structure and which also can be used to address exemplary taxonomic questions. With our work, we start to close the gap of Calcarea in the sponge barcoding project ( and provide a resource for biodiversity studies and potentially for DNA-guided species identification.


Integrative taxonomy Calcareous sponges DNA-barcode LSU rRNA Sponge barcoding database 



We thank Adrian Troya for his assistance in generating the ITS1 sequences used in this study and two anonymous reviewers for their helpful comments.

Supplementary material

13127_2015_247_Fig4_ESM.jpg (5.9 mb)

Specimen images and sections of reference Calcinea. Morphological and Sequence data of shown specimens have been deposited in the sponge barcoding database ( (JPG 5.93 MB)

13127_2015_247_Fig5_ESM.jpg (7 mb)

Specimen images, sections and spicules of reference Calcaronea. Morphological and Sequence data of shown specimens have been deposited in the sponge barcoding database ( (JPG 6.96 MB)

13127_2015_247_MOESM1_ESM.xls (62 kb)
ESM 3 Metadata for included sequences: Species, Taxonomy, Voucher specimen, locality and GenBank accession numbers. (XLS 62 kb)
13127_2015_247_MOESM2_ESM.mase (22 kb)
ESM 4 Alignment of ITS clone sequences of eight specimens of Calcaronea. SSU (18S) rDNA and 5.8S rDNA are annotated. (MASE 21.9 kb)
13127_2015_247_MOESM3_ESM.xls (38 kb)
ESM 5 Sequence lengths of calcinean ITS1 regions. (XLS 37.5 kb)
13127_2015_247_MOESM4_ESM.mase (79 kb)
ESM 6 Alignment of Calcareous Sponge LSU (C-region). Minimum-free energy predictions from the RNAsalsa-output, RNAlifold-predictions and our final structure are included. Additionally, the selected sites for the phylogenetic analyses are saved as a set within the document. (MASE 78.8 kb)


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Copyright information

© Gesellschaft für Biologische Systematik 2015

Authors and Affiliations

  1. 1.Department of Earth and Environmental SciencesLudwig-Maximilians-Universität MünchenMunichGermany
  2. 2.Bayerische Staatssammlung für Paläontologie und GeologieMunichGermany
  3. 3.GeoBio-Center, Ludwig-Maximilians-Universität MünchenMunichGermany

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