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...已知部分濒危物种尽管有效种群规模（effective population size, Nes）极小、遗传多态性水平极低，却已存续数千年。为阐明全基因组遗传多样性对于受威胁物种自然种群长期存续的重要意义，本研究对赤鲈（*Lates japonicus*）——曾被认为凭借极低遗传变异长期存活的物种——开展了全基因组测序。赤鲈的全基因组单核苷酸变异杂合度（single nucleotide variant heterozygosity）经估算为3.3–3.4 × 10^-4 /bp，是硬骨鱼类（teleost fishes）中最低值之一。种群历史动态分析显示，自3万年前至今，赤鲈的有效种群规模（Ne）始终维持在1000左右。然而，对赤鲈基因组遗传多样性的精细分析揭示，多个包含免疫、突触发育及嗅觉感知系统相关基因的基因组区域仍保留了相对较高的核苷酸多态性。Thi..., 赤鲈的染色体级基因组组装通过以下方式生成：利用mScaffolder（Chakraborty等，2018），结合以MUMmer工具包（Kurtz等，2004）中Nucmer将其比对至金鲈（*L. calcarifer*，Vij等，2016）的染色体级基因组组装结果作为引导，对scaffolds（基因组支架序列）进行排序，从而获得该组装结果。本组装的基因预测采用BRAKER1流程（Hoff等，2019）整合的GeneMark-ET（Lomsadze等，2014）与AUGUSTUS（Keller等，2011）工具，基于屏蔽后的基因组序列与RNA测序（RNA-Seq）剪接比对信息完成。 # *Lates japonicus* 染色体级基因组组装与注释 https://doi.org/10.5061/dryad.m37pvmdb6 赤鲈（*Lates japonicus*）的染色体级组装压缩FASTA格式文件与GFF3格式注释文件。 ## 数据与文件结构说明 210531_Akame_5.final.Lcal.chromosomal.sort.fasta.gz：染色体级组装的压缩FASTA格式文件 Lates-japonicus-Ljap2-v1.0.a1-merged-2021-07-09-15-48-11.gff：染色体级组装的GFF3格式注释文件 ## 共享与获取信息 赤鲈的scaffold级基因组组装已提交至日本DNA数据库（DNA Data Bank of Japan, DDBJ），获取编号分别为SAMD00509453（高知县样本）与SAMD00518784（宫崎县样本）。赤鲈的测序读段存档（SRAs）与基因组组装结果（高知县样本：BRZM01000000，宫崎县样本：BAABXA010000000）已存入DDBJ基因组数据库。Chromium关联Illumina读段、RNA测序（RNA-Seq）读段（Illumina[...]