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Behind the Science: Porifera genomics, the trickiness of an early emerging taxon


About the blog author: Yvain Desplat graduated with Master of Science from Nova Southeastern University in Florida (August, 2020). His thesis work focused on characterizing gene responses after oil and dispersant exposure in marine sponges (Cinachyrella spp.) to establish the genus Cinachyrella as a bioindicator in the face of environmental challenges. He currently works as a Research Associate II at JumpCode Genomics Inc in San Diego, California.





Marine sponges (Phylum Porifera) are rarely used as experimental models, but their development as such offers several benefits. Besides occurring in oceans worldwide and being one of the earliest emerging metazoan taxa, sponges have a simple, basic physiology with some features that can mirror more complex animals (Riesgo et al. 2014; Feuda et al. 2017).  However, very little is known about those organisms from a genomics perspective. To date, only two genomes are publicly available: Amphimedon queenslandica (Fernandez-Valverde et al. 2015) and Ephydatia muelleri (Kenny et al. 2020). A. queenslandica was the first ever poriferan genome to be assembled with the colossal worked achieved by Srivastava et al. (2010) and Fernandez-Valverde et al. (2015). These teams showed how tricky the de-novo assembly of the genome and transcriptome of such an understudied phylum really is.

The difficulty in assembling such genomics resources primarily results from two main reasons: a) sponges are known to be highly symbiotic organisms, with some species having symbiotic microbial communities composing large proportions of the sponge biomass (called in the field High Microbial Abundance sponges or HMA), which renders downstream analysis cumbersome, and b) correct identification of specimens is sometimes tricky as even taxonomic genetic markers are not always detected.

Cinachyrella alloclada in acclimation tanks. (photo by Jose V. Lopez)

In our new Journal of Heredity article (Desplat et al, 2022), we decided to study a genus of marine sponges found globally, Cinachyrella, in order to gauge the genetic responses in the face of environmental stress. However, besides the lack of genome or transcriptome resources for this species, three species of Cinachyrella are present on Florida’s reef tract: Cinachyrella alloclada, Cinachyrella apion, and Cinahcyrella kuekenthali. Those three sponge species are all HMA sponges and are easily not distinguishable through the eye (Shuster et al. 2017). Hence, genetic marker analysis is required to characterize the species and perform any study. In Cinachyrella, the Group I intron sequence motif LAGDIGLAD is usually used to call correct taxonomy, but even then, this intron is challenging to PCR amplify and not always present in the samples. The other solution is to use house-keeping genes such as EF1A (elongation factor 1A).

Consequently, in an effort to extend genomics resources for the Phylum Porifera, we here report the assembly of the holo-transcriptome of the HMA sponge Cinachyrella alloclada (identified through EF1A gene characterization). The assembly consisted of 1,194,291 contigs among which a total of 39,813 transcripts identified as sponge related. The large majority of transcripts (36,459) was identified as similar to the sponge Amphimedon queenslandica. Thus, a large difference exists between the number of hits matching a sponge and the total number of annotated genes. This finding could be explained by the well documented presence of microbial symbionts, composing up to 60% of total organismal biomass (Webster and Thomas 2016; Lopez 2019).

Our effort adds a new dataset in the Order Tetractinellida, consistent with previous sponge RNAseq studies (Manousaki et al. 2019) and is available on the NCBI repository under the accession GJAZ00000000 under BioProject PRJNA663558.


Desplat, Y., Warner, J., Lopez, JV. (2022) Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada. Journal of Heredity. esab075

Fernandez-Valverde, S. L., Calcino, A. D., & Degnan, B. M. (2015). Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica.BMC Genomics16(1). doi:10.1186/s12864-015-1588-z

Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., et al. & Pisani, D. (2017). Improved modeling of compositional heterogeneity supports sponges as sister to all other animals. Current Biology, 27(24), 3864-3870.

Kenny, N.J., Francis, W.R., Rivera-Vicéns, R.E. et al. (2020) Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nat Commun 11, 3676

Lopez JV. (2019) After the Taxonomic Identification Phase: Addressing the Functions of Symbiotic Communities within Marine Invertebrates. In Symbionts of Marine Sponges and Corals. Z. Li (ed.), Springer- Verlag. Dordrecht, The Netherlands.  Pp 105-144.

Manousaki T, Koutsouveli V, Lagnel J, Kollias S, Tsigenopoulos CS, Arvanitidis C … Dailianis, T. (2019) A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts. BMC Research Notes, 12:1-3.

Riesgo A, Farrar N, Windsor PJ, Giribet G, Leys SP. (2014) The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges. Molecular Biology and Evolution. 31:1102-1120. 

Schuster A, Lopez JV, Becking LE, Kelly M, Pomponi SA, Wörheide G, … Cárdenas P. (2017) Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding. BMC Evolutionary Biology. 17: doi: 10.1186/s12862-017-0928-9.

Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E., Mitros, T., … & Rokhsar, D. S. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature466(7307), 720-726.

Webster NS, Thomas T. (2016) The Sponge Hologenome. MBio, 7: doi: 10.1128/mbio.00135-16

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