Physiological mechanisms of shell microstructural regulation in Japanese pearl oyster under hypoxic stress: Insights into molluscan resilience against environmental changes
Data files
Jan 06, 2026 version files 36.08 MB
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DEG_list_of_adductor_muscle.csv
119.94 KB
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DEG_list_of_gill.csv
108.32 KB
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DEG_list_of_mantle_edge.csv
173.86 KB
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DEG_list_of_mantle_pallium.csv
243.05 KB
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README.md
4.38 KB
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whole_dataset_of_gene_ontology_mapping.csv
35.43 MB
Abstract
Investigating the anomalous expression of nacre, one of the most common microstructures of the Mollusca, as an environmental archive and its genomic background provides novel insights into sclerochronology and biomineralization. In this study, we aimed to elucidate the physiological responses of the Japanese pearl oyster, Pinctada fucata, under hypoxia, focusing on shell microstructure plasticity. We conducted RNA-seq analysis in specimens from different depths with different oxygen concentrations and observed changes in microstructures. We found differences in shell microstructure and distinct gene expression profiles between hypoxia and normoxia. Several shell matrix protein genes were downregulated under hypoxia, suggesting their role in shell formation. We estimated the dissolved oxygen threshold affecting the physiological resistance of P. fucata to microstructural alterations. These results indicate that molluscan shell microstructures are under genetic controls in response to environmental stressors. Our findings on anomalous nacre may serve as a novel sclerochronological proxy for understanding hypoxic occurrences.
Physiological mechanisms of shell microstructural regulation in Japanese pearl oyster under hypoxic stress: Insights into molluscan resilience against environmental changes, Marine Pollution Bulletin, 2026, DOI: https://doi.org/10.1016/j.marpolbul.2025.119082
Dryad dataset DOI: https://doi.org/10.5061/dryad.pnvx0k6zn
Overview
This dataset contains differential expression (DE) results from RNA-seq of Pinctada fucata under normoxia vs hypoxia, and functional annotation outputs.
Each DEG table is provided per tissue.
Experimental groups (important for interpreting m.value sign)
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G1: normoxia
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G2: hypoxia
Note: In TCC, M = log2(G2) − log2(G1).
File inventory
All files are comma-separated values (CSV) with a header row, UTF-8 encoding.
1) DEG_list_of_adductor_muscle.csv
Rows: one row per gene (gene_id).
Content: DE results from TCC-GUI for adductor muscle.
Inclusion: DEGs only.
Variables (data dictionary)
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gene_id (string): gene/transcript identifier used in the reference transcriptome/annotation.
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a.value (numeric, unitless): A-value from MA plot: A = (log2(G2)+log2(G1))/2 computed from normalized counts.
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m.value (numeric, unitless): M-value from MA plot: M = log2(G2)−log2(G1).
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p.value (numeric): raw p-value for differential expression.
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q.value (numeric): multiple-testing adjusted p-value (FDR; q-value).
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rank (integer): rank of p.value in ascending order (1 = smallest p.value).
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estimatedDEG (integer 0/1): 1 if q.value < [FDR threshold used, e.g., 0.05], else 0.
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SMP (string): genes annotated as shell matrix proteins (SMPs) by local BLAST analysis.This column was manually inserted by the authors. A blank cell indicates no SMP hit was detected.
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Description (string): Top BLAST hit functional description exported from OmicsBox gene ontology mapping. This column was copied from gene ontology mapping result.
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GO IDs (string): OmicsBox gene ontology IDs (prefixed by ontology: P:, F:, C:) associated with the gene. Multiple IDs are separated by ";". This column was copied from gene ontology mapping result.
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GO Names (string): GO term names corresponding to GO IDs, in the same order (separated by ";").
2) DEG_list_of_gill.csv
[same structure as above]
3) DEG_list_of_mantle_edge.csv
[same structure as above]
4) DEG_list_of_mantle_pallium.csv
[same structure as above]
5) whole_dataset_of_gene_ontology_mapping.csv
Content: OmicsBox export of GO mapping/annotation results for the reference gene set.
Variables
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Nr (integer): consecutive row number in OmicsBox result table.
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Tags (string): OmicsBox status tags (e.g., BLASTED/INTERPRO/MAPPED/ANNOTATED).
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SeqName (string): unique sequence name (gene ID).
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Description (string): Description of the top BLAST hit.
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Length (integer): sequence length.
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#Hits (integer): number of BLAST hits.
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e-Value (numeric): lowest e-value among BLAST hits.
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sim mean (numeric): mean similarity among BLAST hits.
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#GO (integer): number of GO terms assigned.
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GO IDs (string): Gene Ontology identifiers assigned to the sequence. GO terms are prefixed by ontology: P: Biological Process, F: Molecular Function, C: Cellular Component.
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GO Names (string): Names/descriptions corresponding to GO IDs. Multiple entries are separated by ";".
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Enzyme Codes (string): Enzyme Commission (EC) numbers inferred from annotation. Multiple entries are separated by ";". Blank indicates no EC number was assigned.
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Enzyme Names (string): Enzyme names corresponding to Enzyme Codes.
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InterPro IDs (string): InterProScan-derived identifiers for protein domains/families and related member database IDs (e.g., PFAM, GENE3D). Multiple entries are separated by ";".
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InterPro GO IDs (string): GO identifiers associated with InterPro entries (ontology-prefixed with P:, F:, C: when provided). Multiple entries are separated by ";". Blank indicates no InterPro-linked GO term was available.
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InterPro GO Names (string): GO term names corresponding to InterPro GO IDs. Multiple entries are separated by ";".
Missing values policy
- If cells are blank (empty), this indicates: not hit.