Assembly of a high-quality Polypterus senegalus diploid genome.

Background: Polypterus senegalus is a major actinopterygian fish that provides vital insights into vertebrate terrestrial adaptation. Advances in sequencing technologies have enabled improvements to the reference genome of P. senegalus, highlighting the need to expand research on this species.

Objective: In this study, we sought to construct high-quality, partially-phased, assemblies of the P. senegalus genome using high-fidelity long-read sequencing data.

Methods: First, partially-phased assemblies of P. senegalus genome using PacBio HiFi data. And then, our assemblies were compared with a previously published genome in terms of total length, contiguity, base-level accuracy, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness, including resolution of repetitive regions and identification of telomere-telomere chromosomes.

Results: Compared with a previously published genome, our assemblies exhibit improved quality in overall quality. A total of 20,940 genes were annotated employing integrated short-read and long-read RNA sequencing data. Transcriptomics revealed the gene-expression relationships between 12 tissue types and the distinct expression patterns of genes associated with key evolutionary traits, such as aerial respiration, angiogenesis, and limb flexibility. Notably, several genes including Tcf21, Foxf1, and Tbx3a were coordinately expressed in the lungs and swim bladder, supporting shared origins and developmental patterns. Analyses of the correlations among tissues revealed physiological similarities between the lungs, kidneys, and spleen.

Conclusion: Our results provide a valuable genomic resource for P. senegalus and offer novel insights into the molecular basis of vertebrate organ evolution and adaptation.