Unknown

Dataset Information

0

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

ABSTRACT: Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, nearly all containing telomeric repeats at their ends. We annotated 31,656 genes and discovered that approximately 2.19% of the genome contained DNA transposon elements repressed within duplicated genes. Analyzing 5-methylcytosine (5mC) modifications using HiFi reads, we observed open/close chromatin patterns at gene promoters, including the FADS2 gene involved in Omega-3 production. This chromosome-level reference genome provides unprecedented opportunities for advancing our knowledge of chub mackerels in biology, industry, and conservation.

SUBMITTER: Lee YH 

PROVIDER: S-EPMC10709322 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, n  ...[more]

Similar Datasets

Unknown Chromosome-level genome assembly of Indo-Pacific king mackerel (Scomberomorus guttatus).
| S-EPMC11561338 | biostudies-literature
Unknown Draft Genome Sequence of Streptomyces sp. Strain RFCAC02, Isolated from the Gut Microflora of the Pacific Chub Mackerel Scomber japonicus peruanus.
| S-EPMC6554607 | biostudies-literature
Unknown A genome assembly of the Atlantic chub mackerel (<i>Scomber colias</i>): a valuable teleost fishing resource.
| S-EPMC9650269 | biostudies-literature
Unknown A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias.
| S-EPMC5996228 | biostudies-literature
Unknown Effect of washing, soaking, and cooking methods on perfluorinated compounds in mackerel (Scomber japonicus).
| S-EPMC7455985 | biostudies-literature
Unknown <i>In vivo</i> antioxidant activity of mackerel (<i>Scomber japonicus</i>) muscle protein hydrolysate.
| S-EPMC6305115 | biostudies-literature
Unknown Genetic investigation of population structure in Atlantic chub mackerel, <i>Scomber colias</i> Gmelin, 1789 along the West African coast.
| S-EPMC11380841 | biostudies-literature
Unknown Population structure of Atlantic mackerel (Scomber scombrus).
| S-EPMC3669354 | biostudies-literature
Unknown De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus).
| S-EPMC10776605 | biostudies-literature
Unknown Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus.
| S-EPMC7874996 | biostudies-literature