Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean
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Published:2023-12-08
Issue:1
Volume:10
Page:
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ISSN:2052-4463
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Container-title:Scientific Data
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language:en
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Short-container-title:Sci Data
Author:
Lee Young HoORCID, Abueg Linelle, Kim Jin-Koo, Kim Young Wook, Fedrigo Olivier, Balacco Jennifer, Formenti GiulioORCID, Howe Kerstin, Tracey Alan, Wood JonathanORCID, Thibaud-Nissen FrançoiseORCID, Nam Bo Hye, No Eun Soo, Kim Hye Ran, Lee ChulORCID, Jarvis Erich D.ORCID, Kim HeebalORCID
Abstract
AbstractChub 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.
Funder
Korea Institute of Marine Science and Technology promotion National Research Foundation of Korea Wellcome Trust Howard Hughes Medical Institute
Publisher
Springer Science and Business Media LLC
Subject
Library and Information Sciences,Statistics, Probability and Uncertainty,Computer Science Applications,Education,Information Systems,Statistics and Probability
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