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


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.

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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.


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


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

Author information




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.

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The authors declare that they have no conflict of interest.

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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.

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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).

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