Molecular Safeguards of Survival: De novo transcriptome assembly and tissue-specific transcriptomic profiling of the yellow-foot clam Paphia malabarica
- 1ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala 682018 India
Abstract
The yellow-foot clam, Paphia malabarica Chemnitz, 1782 is a regionally important fishery and aquaculture resource along the southwest coast of India. The fishery of this species from the Ashtamudi estuary has been certified as sustainable by the Marine Stewardship Council. We generated the first high-quality, comprehensive de novo transcriptome assembly of Paphia malabarica using Illumina paired-end sequencing. A total of 729.2 million raw reads were generated and further processed and assembled using the Trinity assembler. The final assembly yielded 55,980 predicted coding sequences (CDS) with an N50 of 1,605 bp. The BUSCO completeness of the transcriptome assembly was 97.8% against the Metazoa (metazoa_odb10) dataset and 88.52% against the Mollusca (mollusca_odb10) dataset. Functional annotations were performed using UniProt, KEGG, Reactome, InterPro, and eggNOG databases. Out of 56,713 transcripts, 20,624 sequences (36.37%) were annotated with Gene Ontology (GO) terms, yielding 360,305 annotations. Gene ontology and pathway analyses indicated that transcripts associated with key biological processes, such as replication, recombination and repair, transcription, signal transduction mechanisms, posttranslational modification, protein turnover, chaperones, carbohydrate transport and metabolism, and amino acid transport and metabolism, are important for the buried lifestyle of the yellow-foot clam, Paphia malabarica.
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BibTeX
@article{sukumaran2026molecular,
title = {{Molecular Safeguards of Survival: De novo transcriptome assembly and tissue-specific transcriptomic profiling of the yellow-foot clam Paphia malabarica}},
author = {Sandhya Sukumaran and V. G. Vysakh and Wilson Sebastian},
journal = {Scientific Data},
year = {2026},
month = jun,
doi = {10.1038/s41597-026-07761-8},
url = {https://doi.org/10.1038/s41597-026-07761-8},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Molecular Safeguards of Survival: De novo transcriptome assembly and tissue-specific transcriptomic profiling of the yellow-foot clam Paphia malabarica
AU - Sandhya Sukumaran
AU - V. G. Vysakh
AU - Wilson Sebastian
PY - 2026
DA - 2026/06/27
JO - Scientific Data
DO - 10.1038/s41597-026-07761-8
UR - https://doi.org/10.1038/s41597-026-07761-8
AB - The yellow-foot clam, Paphia malabarica Chemnitz, 1782 is a regionally important fishery and aquaculture resource along the southwest coast of India. The fishery of this species from the Ashtamudi estuary has been certified as sustainable by the Marine Stewardship Council. We generated the first high-quality, comprehensive de novo transcriptome assembly of Paphia malabarica using Illumina paired-end sequencing. A total of 729.2 million raw reads were generated and further processed and assembled using the Trinity assembler. The final assembly yielded 55,980 predicted coding sequences (CDS) with an N50 of 1,605 bp. The BUSCO completeness of the transcriptome assembly was 97.8% against the Metazoa (metazoa_odb10) dataset and 88.52% against the Mollusca (mollusca_odb10) dataset. Functional annotations were performed using UniProt, KEGG, Reactome, InterPro, and eggNOG databases. Out of 56,713 transcripts, 20,624 sequences (36.37%) were annotated with Gene Ontology (GO) terms, yielding 360,305 annotations. Gene ontology and pathway analyses indicated that transcripts associated with key biological processes, such as replication, recombination and repair, transcription, signal transduction mechanisms, posttranslational modification, protein turnover, chaperones, carbohydrate transport and metabolism, and amino acid transport and metabolism, are important for the buried lifestyle of the yellow-foot clam, Paphia malabarica.
SN - 2052-4463
ER -