Evidence map›Paper›PMID 35189951›Full record

ArticleGenome biology2022

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Adrien Leger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten and 16 more

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

Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
2.8field-weighted citation impact, top 9% 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

11 citing papers in PubMed, 18 citations in OpenAlex.

  1. Article
  2. Review
  3. MedakaBase as a unified genomic resource platform for medaka fish biology.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025
    Article
  4. Article
  5. Article
  6. Article
  7. Real-time genomics for One Health.Molecular systems biology · 2023
    Review
  8. Article
  9. Article
  10. Article
  11. Characterization ofFrontiers in physiology · 2021
    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

26 authors at 4 institutions in 3 countries.

Adrien Leger *European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Ian Brettell *European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Jack MonahanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Carl BartonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Nadeshda WolfInstitute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
Natalja KusminskiInstitute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
Cathrin HerderInstitute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
Narendar AadepuInstitute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
Clara BeckerCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Jakob GiertenCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Omar T HammoudaCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Eva HaselCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Colin LischikCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Katharina LustCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Natalia SokolovaCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Risa SuzukiCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Tinatini TavhelidseCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Thomas ThumbergerCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Erika TsingosCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Philip WatsonCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Bettina WelzCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Kiyoshi NaruseNational Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan.
Felix LoosliInstitute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
Joachim WittbrodtCentre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany.
Ewan BirneyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Tomas FitzgeraldEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-2370-8496
Heidelberg University · DEEuropean Bioinformatics Institute · GBKarlsruhe Institute of Technology · DENational Institute for Basic Biology · JP

Funding

The medaka Kiyosu panel: dissecting GxE effects of environmental chemicalsR01ES029917 · NIEHS · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI BIRNEY, EWAN, GOLDSTONE, JARED VERRILL · 2019 to 2023
$2.1M
NIEHS NIH HHS R01 ES029917
6 · The paper itself

Abstract

backgroundThe teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals.

resultsWe exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines.

conclusionsWe present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.

Indexed as

OryziasAnimalsEpigenomicsGenomeGenomicsHumansGeneticsGraph genomeInbred panelLong read sequencingMedakaMethylationNanoporePan genomeStructural variation

Identifiers

PMID35189951
PMCPMC8862245
OpenAlexW4225291880

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.