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 (Nes) 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 (Lates japonicus), 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 Ne 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. Thi..., The chromosome-level assembly of Lates japonicus was generated by ordering the scaffolds using mScaffolder (Chakraborty et al. 2018) guided by their alignments to the chromosome-level genome assembly of L. calcarifer (Vij et al. 2016) using Nucmer implemented in MUMmer (Kurtz et al. 2004). Gene predictions in the assembly were carried out using the masked genome and RNA-Seq spliced alignment information by GeneMark-ET (Lomsadze et al. 2014) and AUGUSTUS (Keller et al. 2011) implemented in the BRAKER1 pipeline (Hoff et al. 2019)., , # Chromosome-level assembly and annotation of *Lates japonicus*

[https://doi.org/10.5061/dryad.m37pvmdb6](https://doi.org/10.5061/dryad.m37pvmdb6)

A compressed FASTA format file of the chromosome-level assembly and a GFF3 format annotation file of akame (*Lates japonicus*).

## Description of the data and file structure

210531_Akame_5.final.Lcal.chromosomal.sort.fasta.gz: a compressed FASTA format file of the chromosome-level assembly

Lates-japonicus-Ljap2-v1.0.a1-merged-2021-07-09-15-48-11.gff: a GFF3 format annotation file of the chromosome-level assembly

## Sharing/Access information

The scaffold-level genome assemblies of akame have been submitted to DNA Data Bank of Japan (DDBJ) under the accession number SAMD00509453 (Kochi) and SAMD00518784 (Miyazaki). The sequencing reads archives (SRAs) and the genome assemblies in akame (Kochi: BRZM01000000, Miyazaki: BAABXA010000000) have been deposited in the DDBJ genome database. The Chromium-linked Illumina reads, RNA-Seq reads (Illu...