Data associated with "Predator presence elicits a molecular sensory response in a sponge"
Data files
Jul 08, 2026 version files 118.67 MB
-
Aqueenslandia_gene_models.zip
22.43 MB
-
DGE.zip
12.67 MB
-
README.md
4.94 KB
-
Scripts.zip
10.29 KB
-
Synapse_blast.zip
15.78 KB
-
TOPGO.zip
1.05 MB
-
Transcriptome.zip
82.49 MB
Abstract
Predator-prey interactions in sponges (Porifera) encompass direct and non-consumptive effects, including inducible defenses following non-lethal grazing. It has been hypothesized that the ability to dissolve and burrow into calcium carbonate substrates to live endolithically evolved for predator avoidance in bioeroding sponges. However, the molecular mechanisms that regulate sponge responses to predation and whether bioerosion is an inducible defense, remain poorly understood. We investigated the transcriptomic response of the bioeroding sponge, Cliona celata, to its gastropod predator, Seila adamsii. Sponges were exposed to three treatments: direct predation, predator chemical cues, and a predator-free control. We found that predation and chemical cues elicited significant differential gene expression compared to the control. Upregulation of synaptic genes in response to chemical cues, particularly those expressed in water-pumping choanocytes, suggests they are important primary sensory cells. Conversely, wound healing and extracellular matrix repair functional categories were upregulated in the predation treatment. While we identified the upregulation of functional categories previously implicated in bioerosion, we found no differential expression of carbonic anhydrases, a hypothesized driver of chemical bioerosion. These results demonstrate that despite not having a complete nervous system, C. celata possesses a molecular sensory pathway capable of distinguishing between direct predation and predator chemical cues.
Dataset DOI: 10.5061/dryad.tx95x6bc1
Description of the data and file structure
Files and variables
Archive: Scripts.zip
File: DESeq2.R
Description: R script to test for differential gene expression
File: topgo_DEG.R
Description: R script to test for significantly enriched functional categories in lists of differentially expressed genes
File: topgo_WGCNA.R
Description: R script to test for significantly enriched functional categories in modules of genes identified by the WGCNA
File: WGCNA.R
Description: R script to assign transcripts to modules based on correlated patterns of expression
Archive: Synapse_blast.zip
File: synapse_nuc_blastn
Description: output- output from blastn search of A. queenslandica nucleotide synapse gene models against the Cliona celata nucleotide transcriptome
File: synapse_prot_blastp_output
Description: output from blastp search of A. queenslandica nucleotide synapse gene models against the Cliona celata nucleotide transcriptome
Archive: TOPGO.zip
File: [color]_module3.txt
Description: These files contain lists of transcripts assigned to a given WGCNA module
File: cues_vs_control_deg3.txt
Description: List of translated transcripts differentially expressed in response to chemical cues compared to the control
File: cues_vs_pred_deg3.txt
Description: List of translated transcripts differentially expressed in response to chemical cues compared to direct predation
File: pred_vs_control_deg3.txt
Description: List of translated transcripts differentially expressed in response to predation compared to the control
File: topgo_DEG.R
Description: R script to test for significantly enriched functional categories in lists of differentially expressed genes
File: topgo_WGCNA.R
Description: R script to test for significantly enriched functional categories in modules of genes identified by the WGCNA
File: trans_pep_go_terms2.txtDescription:
List of GO terms assigned to all transcripts in the C. celata translated transcriptome
Archive: Aqueenslandia_gene_models.zip
File: Aqu2.1_cdna_synapse.fasta
Description: Amphimedon queenslandica nucleotide gene models identified by Wong et al. 2019 as being synapse genes
File: Aqu2.1_genes_cdna.fastaDescription:
Amphimedon queenslandica nucleotide gene models
File: Aqu2.1_genes_pep.fasta
Description: Amphimedon queenslandica protein gene models
File: Aqu2.1_pep_synapse.fasta
Description: Amphimedon queenslandica protein gene models identified by Wong et al. 2019 as being synapse genes
Archive: DGE.zip
File: conditions.csv
Description: file containing treatment and sample associations required for DESeq analysis
File: counts_matrix.csv
Description: file generated in RSEM containing read counts for samples generated
File: CUES_DEG_GOTERMS_UNIQUE
Description: file containing gene ontology terms assigned to transcripts differentially expressed in response to chemical cues compared to the control
File: CVP_DEG_GOTERMS_UNIQUE
Description: file containing gene ontology terms assigned to transcripts differentially expressed in response to chemical cues compared to direct predation
File: PRED_DEG_GOTERMS_UNIQUE
Description: file containing gene ontology terms assigned to transcripts differentially expressed in response to direct predation compared to the control
File: DGE_output_chemical_cues.csv
Description: full DESeq2 output for chemical cues compared to the control
File: DGE_output_predation.csv
Description: full DESeq2 output for predation compared to the control
File: DGE_output_cues_vs_predation.csv
Description: full DESeq2 output for chemical cues compared to predation
File: DESeq2.R
Description: R script for differential gene expression analysis
Archive: Transcriptome.zip
File: 3lib_shell_v2.15.kareem.trinity.Trinity.fasta.gene_trans_map
Description: File generated in Trinity that matches transcript isoforms to genes in the transcriptome assembly
File: 3lib_shell_v2.15.kareem.trinity.Trinity.fasta.transdecoder.pep.defs.fa.tsv
Description: Gene ontology terms assigned to translated transcripts in InterProScan
File: cliona_celata_transcriptome_nucleotide.fasta
Description: Trinity transcriptome nucleotide assembly
File: cliona_celata_transcriptome_protein.fasta
Description: Trinity transcriptome protein assembly
File: transcriptome_nuc_to_prot_defline_key.txt
Description: File that matches transcript deflines in the nucleotide transcriptome assembly to transcript deflines in the translated transcriptome assembly
Access information
Other publicly accessible locations of the data:
- Raw sequence data are available on NCBI at accession PRJNA993268
