Chromosome-level assembly and annotation of Lates japonicus

<p>It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes (<em>N</em>_es) and low levels of genetic polymorphisms. To understand the importance of genome-wide genetic diversity for the long-term persistence of natural populations in threatened species, we determined the whole genome sequences of akame (<em>Lates japonicus</em>), which is considered to have survived a long time with extremely low genetic variations. Genome-wide single nucleotide variant heterozygosity in akame was estimated to be 3.3–3.4 × 10^-4 /bp, one of the smallest values in teleost fishes. Analysis of demographic history inferred that the <em>N</em>_e in akame was around 1,000 from 30,000 years ago to the recent past. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions containing genes involved in immunity, synaptic development, and olfactory sensory systems have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential in fluctuating environments. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, indicating that adaptive evolution to the temperate waters has occurred after the speciation of akame and its close relative, barramundi (<em>L. calcarifer</em>). Our results indicated that the functional genetic diversity in akame likely contributed to avoiding the harmful effects of the reduced population size, despite the increased genetic load in this species.</p>