A tale of two sisters: De novo genome assembly and comparative genomic analysis of two Decapterus species, D. macarellus and D. macrosoma

Title : A tale of two sisters: De novo genome assembly and comparative genomic analysis of two Decapterus species, D. macarellus and D. macrosoma

Abstract:

Round scads (Decapterus spp.) are highly migratory pelagic fishes that support major fisheries throughout Southeast Asia, including the Philippines. The close morphological similarity among species within this genus complicates taxonomic identification, particularly for the sister species shortfin scad (D. macarellus) and mackerel scad (D. macrosoma). Despite their ecological and economic importance, genomic resources for Decapterus remain limited, hindering comparative genomic studies that could elucidate patterns of genetic divergence, evolutionary relationships, and adaptive traits.

Here, we present the first de novo genome assemblies of D. macarellus and D. macrosoma. The D. macarellus assembly comprised 1,477 contigs with an N50 of 1.88 Mb and a total size of 674 Mb, while the D. macrosoma assembly contained 440 contigs, with an N50 of 20.45 Mb and a total size of 718 Mb. Genome completeness was high for both assemblies, with BUSCO scores of 98.1% for D. macarellus and 98.3% for D. macrosoma based on 3,640 single-copy orthologs from the Actinopterygii_odb10 lineage dataset. Repetitive elements accounted for 25.86% and 29.30% of the D. macarellus and D. macrosoma assemblies, respectively. Genome annotation identified 25,733 protein-coding genes in D. macarellus and 26,680 in D. macrosoma, with approximately 99% functionally annotated in both species. Synteny analysis revealed a high level of collinearity between the two genomes, while also identifying several structural variations, including inversions and translocations. Furthermore, phylogenomic analyses revealed incongruence between mitochondrial and nuclear genome-based trees, suggesting uncertainty in the current placement of these species as sister taxa.

These high-quality genomic resources provide a foundation for comparative and evolutionary studies of round scads, advancing our understanding of their biology and ultimately contributing to sustainable fisheries management of this economically important genus.

Biography:

I am a graduate student pursuing a master’s degree in marine science at The Marine Science Institute, University of the Philippines Diliman. My research interests focus on the genetics and genomics of marine organisms, including seaweeds, shrimps, fishes, and environmental DNA (eDNA). I previously worked as a Research Associate, where I developed experience in laboratory research, field sampling, and bioinformatics analysis of next-generation sequencing (NGS) data. Through this, I have contributed to studies on fish and seaweed phylogenetics and shrimp genomics. I have also served as a research technical consultant, providing technical support and conducting workshops for researchers and students.