Skip to main content
Dryad

Chromosome-level assembly and annotation of Lates japonicus

Cite this dataset

Hashiguchi, Yasuyuki (2024). Chromosome-level assembly and annotation of Lates japonicus [Dataset]. Dryad. https://doi.org/10.5061/dryad.m37pvmdb6

Abstract

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.

README: Chromosome-level assembly and annotation of Lates japonicus

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.

Methods

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).

Funding

Ministry of Education, Culture, Sports, Science and Technology