DOI: 10.5061/dryad.m37pvmdb6
title: Chromosome-level assembly and annotation of Lates japonicus

description: 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.
description: The chromosome-level assembly of <em>Lates
 japonicus</em> was generated by ordering the scaffolds using
 mScaffolder (Chakraborty et al. 2018) guided by their alignments to the
 chromosome-level genome assembly of <em>L. calcarifer</em>
 (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).
description: # 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 (Illumina HiSeq), and Nanopore reads utilized for the genome assembly have been deposited to DDBJ sequence read archive (DRA) under the BioProject accession number PRJDB13763.