Functional genomic insights into the recently resurrected Noah’s giant clam tridacna noae röding, 1798 (Cardiidae: Tridacninae): Key genes for immunity and environmental adaptation an in silico study

Date of Publication

7-2025

Document Type

Bachelor's Thesis

Degree Name

Bachelor of Science in Biology major in Medical Biology

Subject Categories

Genetics and Genomics

College

College of Science

Department/Unit

Biology

Thesis Advisor

Jane Abigail M. Santiago

Defense Panel Chair

John Paul S. Domingo


Defense Panel Member

Shad Natthew S. Arce
John Martin S. Mondragon

Abstract (English)

Tridacna noae, a symbiotic giant clam vital to coral reef ecosystems, remains genomically understudied, with no species-specific reference genome available to date. This limits molecular investigations into its physiology, resilience, and ecological role. To address this, we performed the first functional annotation of Tridacna noae using publicly available whole-genome sequencing data. Raw reads were quality-filtered and assembled de novo; gene prediction was carried out using AUGUSTUS, followed by functional annotation via BLASTp, Gene Ontology (GO), InterProScan, KEGG, and eggNOG-mapper. A total of 5,628 protein-coding genes were identified, with enriched functions in oxidative stress response, immune signaling, and symbiosis regulation. Partial representation of the cysteine and methionine metabolism pathway suggested potential for glutathione-based redox buffering. Immune-related genes—including TRIM71-like E3 ligases and beta-arrestins—were also detected, indicating mechanisms for pathogen defense and host-symbiont modulation. BLASTp results revealed significant alignment with mollusks, Symbiodinium spp., and sulfur-oxidizing bacteria, reflecting a complex holobiont structure. These findings underscore the need for de novo genome sequencing and transcriptomic validation to support further functional, ecological, and conservation research on Tridacna noae.

Abstract Format

html

Abstract (Filipino)

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Abstract Format

html

Language

English

Format

Electronic

Keywords

Giant clams; Genomics

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Embargo Period

8-8-2025

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