Scientific data · 2023
Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.
DatasetСтатьяПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод в очереди
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Lee Young Ho, Abueg Linelle, Kim Jin-Koo, Kim Young Wook, Fedrigo Olivier, Balacco Jennifer, Formenti Giulio, Howe Kerstin, Tracey Alan, Wood Jonathan, Thibaud-Nissen Françoise, Nam Bo Hye, No Eun Soo, Kim Hye Ran, Lee Chul, Jarvis Erich D, Kim Heebal
Аннотация
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.