Skip to main content

De novo transcriptome assembly for two color types of the marine sponge Mycale (Carmia) cecilia

Abstract

Despite the ecological importance and the potential pharmacological application of the sponge Mycale (Carmia) cecilia, it is uncertain whether the body-color variation, even in individuals coexisting in the same area, is due to intraspecific phenotypic plasticity or corresponds to taxonomic divergence. This uncertainty is relatively common in several Porifera groups, which lack the resolution of morphological diagnostic characters and slow-evolving mitochondrial genomes as occurs in early splitting lineages. We sequenced the RNA of six individuals with two different body-color (green-morphotype and red-morphotype) collected at the same time side by side. High-throughput sequencing of cDNA libraries produced ~ 129 million reads with a length of 150 bp. Each morphotype was assembled separately owing to the low overlapping in the global assembly. Metatranscriptome de novo assembly of the trimmed and normalized reads produced 461 thousand transcripts for the green-morphotype and 342 thousand for the red-morphotype (respectively). Over 30% of the transcripts contained Open Reading Frames (ORFs) with functional significance. BUSCO analysis of the ORFs of putative poriferan origin (31.3% green or 30.4% red) indicated that our assemblies are 60% complete. This is the first attempt to evaluate the morphological diversity in the species M. (C.) cecilia and the phylum Porifera at the transcriptomic level. Due to the minimum overlap of the assembly and that, the red-morphotype diverged significantly from the green-morphotype (original color of M. (C.) cecilia). Therefore, we suggest that the red-morphotype should undergo a complete taxonomic investigation and its taxonomic status be reviewed. We expect that the transcriptome assembly metrics can be useful for comparing other transcriptome assemblies of non-model organisms.

This is a preview of subscription content, access via your institution.

Data Availability

The mRNA transcriptome datasets for each sample of Mycale (Carmia) cecilia green-morphotype and Mycale (Carmia) aff. cecilia red-morphotype are available under NCBI BioProject PRJNA678333.

References

  1. 1.

    Cruz-Barraza JA, Carballo JL (2008) Taxonomy of sponges (Porifera) associated with corals from the Mexican Pacific Ocean. Zool Stud 47:741–758

    Google Scholar 

  2. 2.

    Ortega MJ, Zubía E, Sánchez MC et al (2004) Structure and cytotoxicity of new metabolites from the sponge Mycale cecilia. Tetrahedron 60:2517–2524. https://doi.org/10.1016/j.tet.2004.01.056

    CAS  Article  Google Scholar 

  3. 3.

    de Laubenfels MW (1936) A comparison of the shallow-water sponges near The Pacific and of The Panama Canal with those at The Caribbean end. Proc United States Natl Museum 83:441–466

    Article  Google Scholar 

  4. 4.

    de Laubenfels MW (1950) The sponges of Kaneohe Bay, Oahu. Pacific Sci 4:3–36

    Google Scholar 

  5. 5.

    Burgsdorf I, Erwin PM, López-Legentil S et al (2014) Biogeography rather than association with cyanobacteria structures symbiotic microbial communities in the marine sponge Petrosia ficiformis. Front Microbiol 5:1–11. https://doi.org/10.3389/fmicb.2014.00529

    Article  Google Scholar 

  6. 6.

    Loh TL, López-Legentil S, Song B, Pawlik JR (2012) Phenotypic variability in the Caribbean Orange Icing sponge Mycale laevis (Demospongiae: Poecilosclerida). Hydrobiologia 687:205–217. https://doi.org/10.1007/s10750-011-0806-1

    CAS  Article  Google Scholar 

  7. 7.

    Shaffer MR, Davy SK, Bell JJ (2019) Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification. Heredity (Edinb) 122:354–369. https://doi.org/10.1038/s41437-018-0134-6

    CAS  Article  Google Scholar 

  8. 8.

    Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66:167–174. https://doi.org/10.1007/s00239-008-9069-5

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Andrews S (2010) FastQC A quality control tool for high throughput sequence data. Babraham Bioinformatics. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

  10. 10.

    Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512. https://doi.org/10.1038/nprot.2013.084

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Seppey M, Manni M, Zdobnov EM (2019) BUSCO: Assessing genome assembly and annotation completeness. Methods Mol Biol 1962:227–245. https://doi.org/10.1007/978-1-4939-9173-0_14

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

The first author benefited from a post-doctoral fellowship from UNAM-DGAPA at UNAM-ICMyL.

Funding

This work has been funded by the Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica PAPIIT (DGAPA): PAPIIT-UNAM IN210018.

Author information

Affiliations

Authors

Contributions

All authors conceived and designed the experiments; All authors performed sampling and processing laboratory; José Antonio Cruz-Barraza identified the specimens in situ and laboratory; Ana Castillo-Páez and Raul Llera-Herrera analyzed the data; Ana Castillo-Páez wrote the manuscript; All the authors read, commented and approved on the manuscript.

Corresponding author

Correspondence to José Antonio Cruz-Barraza.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Mycale (Carmia) cecilia is not an endangered or a protected species in the sampling area. Sampling activities were not performed at locations where specific permission is required. This article does not contain any other studies with human participants or animals performed by any authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Castillo-Páez, A., Llera-Herrera, R. & Cruz-Barraza, J.A. De novo transcriptome assembly for two color types of the marine sponge Mycale (Carmia) cecilia. Mol Biol Rep 48, 3023–3026 (2021). https://doi.org/10.1007/s11033-021-06274-4

Download citation

Keyword

  • Genus Mycale
  • RNA-seq
  • Porifera
  • Metatranscriptome
  • Phenotypic variability
  • Taxonomic divergence