Organisms Diversity & Evolution

, Volume 17, Issue 1, pp 111–119 | Cite as

Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis

  • Ricardo C. Neves
  • Joao C. Guimaraes
  • Sebastian Strempel
  • Heinrich Reichert
Original Article


Cycliophorans are characterized by a complex life cycle that involves an asexual generation and a sexual generation. The most prominent life cycle stage in both generations is the so-called feeding stage. Using RNA-Seq, we profiled differential gene expression between feeding stages from asexual and sexual generations to study this intergenerational shift. For this, we also generated a reference transcriptome for the cycliophoran Symbion pandora. We found that a total of 2660 contigs (more than 10% of the total transcriptome) correspond to genes that are expressed differentially in the feeding stages from the asexual generation as compared to the sexual feeding stages. Among these, 1236 genes are upregulated in the asexual stages as compared to the sexual stages. Conversely, 1424 genes are upregulated in the sexual stages as compared to the asexual stages. The asexual stages express genes predominantly related to RNA processing and splicing as well as protein folding, which suggests a high degree of regulation at the transcriptional and post-transcriptional levels. In marked contrast, the sexual stages highly express genes related to signal transduction and neurotransmission. This is the first time that a large whole-transcriptome RNA-Seq expression dataset has been generated for any cycliophoran. Moreover, this study provides important information for further studies on the molecular mechanisms that are involved in the shift from asexual to sexual generations in this still enigmatic group.


Sexual vs. asexual reproduction Life cycle Transcriptomics RNA sequencing Spiralia Lophotrochozoa 



We are grateful to the generous support by the staff from The Sven Lovén Centre for Marine Sciences at the University of Gothenburg. The authors also thank Birgitte Rubak and Stine Elle (both Copenhagen) for providing the line drawings. We thank Kevin Kocot (University of Alabama, USA) for his helpful comments on a preliminary version of this article.

Author’s contributions

RCN and HR conceived of the study and participated in its design and coordination and drafted the manuscript. RCN is the main coordinator of the project, prepared the material for sequencing, coordinated the molecular genetic studies and analysed the data. SS analysed the data. JCG performed statistical analysis and helped to draft the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

13127_2016_315_MOESM1_ESM.tif (4.9 mb)
Supplementary Figure 1. The hypothetical life cycle of Symbion pandora (from Neves et al., 2012; modified after Obst and Funch, 2003). (TIFF 5012 kb)
13127_2016_315_Fig7_ESM.gif (221 kb)

High resolution image (GIF 221 kb)

13127_2016_315_MOESM2_ESM.tif (166 kb)
Supplementary Figure 2. (A) Number of annotated contigs as a function of the stringency of the E-value threshold applied. Note that the lower the E-value, the more similar is the match between the contig and the annotated gene. (B) BLAST annotation of transcriptome assembly for E-values ≤1 × 10−5. Note that 14,541 contigs have high similarity with known proteins. (TIFF 166 kb)
13127_2016_315_Fig8_ESM.gif (45 kb)

High resolution image (GIF 45 kb)

13127_2016_315_MOESM3_ESM.tif (368 kb)
Supplementary Figure 3. Annotation of transcriptome assembly. Bar charts represent the level of similarity to proteins that belong to other (A) genera and (B) species. (TIFF 367 kb)
13127_2016_315_Fig9_ESM.gif (33 kb)

High resolution image (GIF 33 kb)

13127_2016_315_MOESM4_ESM.tif (589 kb)
Supplementary Figure 4. Annotation of transcriptome assembly. Bar charts represent the categorization of the contigs (E-values ≤1 × 10−5) into functional groups belonging to three main GO ontologies: (A) biological processes, (B) molecular functions and (C) cellular components. (TIFF 588 kb)
13127_2016_315_Fig10_ESM.gif (72 kb)

High resolution image (GIF 72 kb)

13127_2016_315_MOESM5_ESM.xlsx (4 mb)
Supplementary Table 1. List of all BLAST hits for the long open reading frames (ORF) predicted for the contigs present in the reference transcriptome. The table shows the following information for each of the long ORFs: Swiss-Prot accession and description of the protein hit, BLAST hit statistics such as percent identity, alignment length, mismatches, gap opens, E-value and bit score. The next columns for each ORF list associated IDs from different publicly available databases (EMBL, Ensembl and RefSeq). The last two columns of the table show the KEGG and GO IDs which could be associated with the Swissprot protein hit by the queried ORF. All IDs are formatted as hyperlinks into the respective databases for easy reference. (XLSX 4084 kb)
13127_2016_315_MOESM6_ESM.xlsx (4.9 mb)
Supplementary Table 2. List of all differentially expressed contigs/transcripts during the life cycle of Symbion pandora. We find 2660 genes that are significantly differentially expressed (P-adjusted <0.01) in the feeding stages from the asexual generation as compared to the sexual feeding stages. Among these, 1424 genes are upregulated in the sexual stages as compared to the asexual stages (upper part of the table). Conversely, 1236 genes are upregulated in the asexual stages as compared to the sexual stages (lower part of the table). Gene ontology (GO) class, description, and official GO identifier are listed for all the genes for which we were able to identify homologues in other species. Note that each contig appears as many times as it is assigned to a GO term. (XLSX 5031 kb)


  1. Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq—a python framework to work with high-throughput sequencing data. Bioinformatics, 31(2), 166–169.CrossRefPubMedGoogle Scholar
  2. Baker, J. M., & Giribet, G. (2007). A molecular phylogenetic approach to the phylum Cycliophora provides further evidence for cryptic speciation in Symbion americanus. Zoologica Scripta, 36, 353–359.CrossRefGoogle Scholar
  3. Baker, J. M., Funch, P., & Giribet, G. (2007). Cryptic speciation in the recently discovered American cycliophoran Symbion americanus; genetic structure and population expansion. Marine Biology, 151, 2183–2193.CrossRefGoogle Scholar
  4. Castro, M. (1992). A methodology for obtaining information on the age structure and growth rates of the Norway lobster, Nephrops norvegicus (L.) (Decapoda, Nephropoidea). Crustaceana, 63, 29–43.CrossRefGoogle Scholar
  5. Funch, P. (1996). The chordoid larva of Symbion pandora (Cycliophora) is a modified trochophore. Journal of Morphology, 230, 231–263.CrossRefGoogle Scholar
  6. Funch, P., & Kristensen, R. M. (1995). Cycliophora is a new phylum with affinities to Entoprocta and Ectoprocta. Nature, 378, 711–714.CrossRefGoogle Scholar
  7. Funch, P., & Kristensen, R. M. (1997). Cycliophora. In F. W. Harrison & R. M. Woollacott (Eds.), Microscopic anatomy of invertebrates, lophophorates, entoprocta and cycliophora (Vol. 13, pp. 409–474). New York: Wiley-Liss.Google Scholar
  8. Funch, P., & Kristensen, R. M. (1999). Cycliophora. In E. Knobil & J. D. Neill (Eds.), Encyclopaedia of reproduction (Vol. 1, pp. 800–808). New York: Academic.Google Scholar
  9. Funch, P., Thor, P., & Obst, M. (2008). Symbiotic relations and feeding biology of Symbion pandora (Cycliophora) and Triticella flava (Bryozoa). Vie et Milieu, 58, 185–188.Google Scholar
  10. Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology, 29, 644–652.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Langmead, B., & Salzberg, S. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Neves, R. C., & Reichert, H. (2015). Microanatomy and development of the dwarf male of Symbion pandora (phylum Cycliophora): new insights from ultrastructural investigation based on serial section electron microscopy. PloS One, 10, e0122364.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Neves, R. C., Cunha, M. R., Kristensen, R. M., & Wanninger, A. (2010a). Comparative myoanatomy of cycliophoran life cycle stages. Journal of Morphology, 271, 596–611.PubMedGoogle Scholar
  15. Neves, R. C., Cunha, M. R., Funch, P., Wanninger, A., & Kristensen, R. M. (2010b). External morphology of the cycliophoran dwarf male: a comparative study of Symbion pandora and S. americanus. Helgoland Marine Research, 64, 257–262.CrossRefGoogle Scholar
  16. Neves, R. C., Kristensen, R. M., & Funch, P. (2012). Ultrastructure and morphology of the cycliophoran female. Journal of Morphology, 273, 850–869.CrossRefPubMedGoogle Scholar
  17. Neves, R. C., Bailly, X., & Reichert, H. (2014). Are copepods secondary hosts of Cycliophora? Organisms Diversity & Evolution, 14, 363–367.CrossRefGoogle Scholar
  18. Obst, M., & Funch, P. (2003). Dwarf male of Symbion pandora (Cycliophora). Journal of Morphology, 255, 261–278.CrossRefPubMedGoogle Scholar
  19. Obst, M., & Funch, P. (2006). The microhabitat of Symbion pandora (Cycliophora) on the mouthparts of its host Nephrops norvegicus (Decapoda: Nephropidae). Marine Biology, 148, 945–951.Google Scholar
  20. Obst, M., Funch P., & Giribet G. (2005). Hidden diversity and host specificity in cycliophorans: a phylogeographic analysis along the North Atlantic and Mediterranean Sea. Molecular Ecology, 14, 4427–4440. Google Scholar
  21. Obst, M., Funch, P., & Kristensen, R. M. (2006). A new species of Cycliophora from the mouthparts of the American lobster, Homarus americanus (Nephropidae, Decapoda). Organisms Diversity & Evolution, 6, 83–97.CrossRefGoogle Scholar
  22. Wanninger, A., & Neves, R. C. (2015) Cycliophora. In A. Wanninger (Ed.), Evolutionary developmental biology of invertebrates (Vol. 2: Lophotrochozoa (Spiralia), pp. 79–87). Wien: Springer-Verlag.Google Scholar

Copyright information

© Gesellschaft für Biologische Systematik 2016

Authors and Affiliations

  • Ricardo C. Neves
    • 1
  • Joao C. Guimaraes
    • 1
  • Sebastian Strempel
    • 2
  • Heinrich Reichert
    • 1
  1. 1.BiozentrumUniversity of BaselBaselSwitzerland
  2. 2.Microsynth AGBalgachSwitzerland

Personalised recommendations