Evidence map›Paper›PMID 38066002›Full record

ArticleScientific data2023

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

Young Ho Lee, Linelle Abueg, Jin-Koo Kim, Young Wook Kim, Olivier Fedrigo, Jennifer Balacco, Giulio Formenti, Kerstin Howe, Alan Tracey, Jonathan Wood and 7 more

Open access · goldAbstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.5field-weighted citation impact, top 32% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Epigenomic methylome landscape of promoters in vertebrate genomes.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 7 institutions in 4 countries.

Young Ho Lee *Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.ORCID 0000-0001-8088-5694
Linelle Abueg *Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA.
Jin-Koo KimDepartment of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea.
Young Wook KimInterdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
Olivier FedrigoVertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA.
Jennifer BalaccoVertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA.
Giulio FormentiVertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA.ORCID 0000-0002-7554-5991
Kerstin HoweTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
Alan TraceyTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
Jonathan WoodTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.ORCID 0000-0002-7545-2162
Françoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-4957-7807
Bo Hye NamBiotechnology Research Division, National Institute of Fisheries Science, Haean-ro 216, Gijang-eup, Gijang-gun, Busan, 46083, Korea.
Eun Soo NoBiotechnology Research Division, National Institute of Fisheries Science, Haean-ro 216, Gijang-eup, Gijang-gun, Busan, 46083, Korea.
Hye Ran KimPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Chul LeeInterdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. clee03@mail.rockefeller.edu.ORCID 0000-0002-9403-0774
Erich D JarvisVertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA. ejarvis@rockefeller.edu.ORCID 0000-0001-8931-5049
Heebal KimInterdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. heebal@snu.ac.kr.ORCID 0000-0003-3064-1303
Seoul National University · KRRockefeller University · USWellcome Sanger Institute · GBNational Institute of Fisheries Science · KRHoward Hughes Medical Institute · USNational Institutes of Health · USPukyong National University · KR

Funding

Wellcome TrustWellcome Trust 206194
6 · The paper itself

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.

Indexed as

CyprinidaeGenomePerciformesAnimalsChromosomesPacific Ocean

Identifiers

PMID38066002
PMCPMC10709322
OpenAlexW4389485687

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.