De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics

The lined sole, Achirus lineatus, is a widely distributed species in the Gulf of Mexico. This basin is constantly exposed to hydrocarbon contamination due to natural oil seeps, oil extraction and oil spills. Previous studies suggest the line sole A. lineatus as a possible sentinel species for oil spills; but the overall landscape of xenobiotic metabolism in this species remains poorly understood. Access to high-quality reference genomes will improve this situation. Here, we report the first whole-genome sequence, assembly, and annotation of the lined sole A. lineatus. We generated 132 Gb of PacBio High-Fidelity (HiFi) reads, which were filtered to retain 93 Gb of ultra-high-quality data. The assembly resulted in a mitogenome of 16,579 bp and a nuclear genome of 486.3 Mb distributed across 199 contigs, with a contig N50 of 9.87 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis based on the actinopterygii_odb10 database (3,640 orthologs) identified 3,611 (99.2%) complete BUSCOs. Genome annotation strategy resulted in the identification of 22,412 protein-coding genes with a high percentage (95.94%) of functional annotation. The genome of A. lineatus revealed 693 expanded and 3349 contracted gene families. We also identified 123 genes involved in the xenobiotics biodegradation and metabolism pathways, as well as neuroplasticity-related genes that may be associated with responses to environmental toxicants, providing baseline genomic information that suggests an integrated adaptive strategy involving both metabolic and nervous system processes. This assembly represents a valuable genomic resource for future toxicological and ecological studies of this species.