{"refrec":{"BRefID":380544,"RR":"<b>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.</b> (2023). Chromosome-level genome assembly of chub mackerel <i>(Scomber japonicus</i>) from the Indo-Pacific Ocean. <i>Scientific Data 10(1)</i>: 880. <a href=\"https://dx.doi.org/10.1038/s41597-023-02782-z\" target=\"_blank\">https://dx.doi.org/10.1038/s41597-023-02782-z</a>","BEntID":378285,"PublicFlag":1,"CheckedFlag":0,"wosflag":1,"vabbflag":0,"RefStringPartII":". <i>Scientific Data 10(1)</i>: 880. <a href=\"https://dx.doi.org/10.1038/s41597-023-02782-z\" target=\"_blank\">https://dx.doi.org/10.1038/s41597-023-02782-z</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":1,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"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.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Lee, Y.H. <i>et al.</i>","Englishabstract":"Chub mackerels (<i>Scomber japonicus</i>) 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 <i>FADS2</i> 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.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Chromosome-level genome assembly of chub mackerel <i>(Scomber japonicus</i>) from the Indo-Pacific Ocean","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2024-12-10 01:33:17.368041","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":null,"OtherDescriptors":null,"Notes":null,"AnaPub":2023,"MonPub":null,"DateUpdate":"2024-01-08","DateCreate":"2024-01-08","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:001118016800002","VABBcode":null,"OpenAcc":1,"DOI":"10.1038/s41597-023-02782-z"},"refs":null,"anarec":{"AnaID":380544,"PubliDate":2023,"Pagination":"880","XtraPublOfAnaID":null,"ISBN":null,"Volume":"10","Issue":"1","BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":254705,"SerRR":"Scientific Data. 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