Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean
Lee, Y.H.; Abueg, L.; Kim, J.-K.; Kim, Y.W.; Fedrigo, O.; Balacco, J.; Formenti, G.; Howe, K.; Tracey, A.; Wood, J.; Thibaud-Nissen, F.; Nam, B.H.; No, E.S.; Kim, H.R.; Lee, C.; Jarvis, E.D.; Kim, H. (2023). Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Scientific Data 10(1): 880. https://dx.doi.org/10.1038/s41597-023-02782-z
In: Scientific Data. Nature Publishing Group: London. ISSN 2052-4463; e-ISSN 2052-4463, more
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| Authors | | Top |
- Lee, Y.H.
- Abueg, L.
- Kim, J.-K.
- Kim, Y.W.
- Fedrigo, O.
- Balacco, J.
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- Formenti, G.
- Howe, K.
- Tracey, A.
- Wood, J.
- Thibaud-Nissen, F.
- Nam, B.H.
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- No, E.S.
- Kim, H.R.
- Lee, C.
- Jarvis, E.D.
- Kim, H.
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| 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. |
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