Chromosome-level genome assembly and genome-wide characterisation of fox gene family in the asian green mussel (Perna viridis): insights into evolution and aquaculture genomics

Vysakh, V G and Sukumaran, Sandhya and Gopalakrishnan, A (2025) Chromosome-level genome assembly and genome-wide characterisation of fox gene family in the asian green mussel (Perna viridis): insights into evolution and aquaculture genomics. In: Book of Abstracts, Department of Marine Biology, Microbiology and Biochemistry. Cochin University of Science and Technology (CUSAT), Kochi, p. 78. ISBN 978-81-986788-9-8

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Abstract

Marine Biotechnology, Fish Nutrition and Health Division, CMFRI, Kerala Mangalore University. Mangalagangotri. Mangalore. Karnataka, India Email: vishakyg99@gmail.com The Asian green musel. Perna viridis is an ecologically and economically significant bivalve species in aquaculture. We build a high-quality chromosome-level genome assembly of P. viridis, generated using PacBio SMRT sequencing, Illumina short read sequencing, Hi-C scaffolding, and Bionano optical mapping. The final assembly. spans 723.49 Mb with a scaffold N50 of 49.74 Mb, anchoring 99% of the genome into 15 chromosomes. A total of 49,654 protein-coding genes were identified. Using this genomic resource, we performed a comprehensive genome-wide characterisation of the Forchead bos (FOX) gene family, which plays a pivotal role in cellular regulation, development, and environmental adaptation. We identified 28 PvFox genes classified into 12 subfamilies, with lineage specific losses of Foxl and FoxQ1. Gene duplication in FoxLI, FoxB1, FoxHI, and FoxD2 suggests adaptive diversification in response to marine stressors. Structural analysis revealed cxan-intron variations, with some PvFox genes exhibiting intron loss, potentially facilitating regulatory plasticity. Phylogenetic analysis confirmed evolutionary conservation, while selection pressure analysis indicated strong purifying selection. GO enrichment highlighted FOX involvement in apoptosis, oxidative stress, and immune responses, reinforcing their functional significance in stresa tolerance and disease resistance. This study provides the first FOX gene landscape in P. viridis advancing our understanding of its adaptive success and offering insights into the evolutionary dynamics of key regulatory genes in marine bivalves.

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