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Lee YH, Abueg L, Kim JK, Kim YW, Fedrigo O, Balacco J, Formenti G, Howe K, Tracey A, Wood J, Thibaud-Nissen F, Nam BH, No ES, Kim HR, Lee C, Jarvis ED, Kim H. Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Sci Data 2023; 10:880. [PMID: 38066002 PMCID: PMC10709322 DOI: 10.1038/s41597-023-02782-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
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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Affiliation(s)
- Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Young Wook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bo Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Haean-ro 216, Gijang-eup, Gijang-gun, Busan, 46083, Korea
| | - Eun Soo No
- Biotechnology Research Division, National Institute of Fisheries Science, Haean-ro 216, Gijang-eup, Gijang-gun, Busan, 46083, Korea
| | - Hye Ran Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, NY, 10065, USA.
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- eGnome inc., C-1008, H Businesspark, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea.
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
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Toy JA, Bernardi G. A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. J Hered 2023; 114:404-409. [PMID: 36790952 PMCID: PMC10287144 DOI: 10.1093/jhered/esad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.
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Affiliation(s)
- Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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