Chromosome-level assembly and annotation of Lates japonicus

It is known that some endangered species have persisted for thousands of
years despite their very small effective population sizes and low levels
of genetic polymorphisms. To understand the genetic mechanisms of
long-term persistence in threatened species, we determined the whole
genome sequences of akame (Lates japonicus), which has survived for a long
time with extremely low genetic variations. Genome-wide 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 revealed that the
effective population size in akame was around 1,000 from 30,000 years ago
to the recent past. The relatively high ratio of nonsynonymous to
synonymous heterozygosity in akame indicated an increased genetic load.
However, a detailed analysis of genetic diversity in the akame genome
revealed that multiple genomic regions, including 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. Analysis of synonymous and nonsynonymous nucleotide
substitution rates has detected signs of positive selection in many akame
genes, suggesting adaptive evolution to temperate waters after the
speciation of akame and its close relative, barramundi (L. calcarifer).
Our results indicate that the functional genetic diversity likely
contributed to the long-term persistence of this species by avoiding the
harmful effects of the population size reduction.