ArticlePLoS computational biology2015
Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 171 citations in OpenAlex.
- Integration of Large-Scale Genomic Data Sources With Evolutionary History Reveals Novel Genetic Loci for Congenital Heart Disease.Circulation. Genomic and precision medicine · 2019Pooled it
- p190A/ARHGAP35 and p190B/ARHGAP5 proteins in endometrial cancer: a novel cancer-relevant paralog interplay.Molecular oncology · 2026Article
- A comprehensive and accessible database of jawed-vertebrate ohnologs.Science advances · 2026Article
- The molecular evolution of vertebrate organs.Nature ecology & evolution · 2026Review
- Copy Number Variants and Their Association With Intracerebral Hemorrhage Risk: A Case-Control Study.Annals of clinical and translational neurology · 2026Article
- Assessing the Impact of Whole Genome Duplication on Gene Expression and Regulation During Arachnid Development.Genome biology and evolution · 2025Article
- Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.Nature communications · 2025Article
- Allelic Imbalance and Chromothripsis Lead to Diversity in Japanese Tumor Genomes With Whole-Genome Duplication.Cancer science · 2025Article
- Whole Genome Duplication in the Genomics Era: The Hidden Gems in Invertebrates?Genome biology and evolution · 2025Review
- Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryotes.Science China. Life sciences · 2025Article
- A metric and its derived protein network for evaluation of ortholog database inconsistency.BMC bioinformatics · 2025Article
- Clinical Potential of Misshapen/NIKs-Related Kinase (MINK) 1-A Many-Sided Element of Cell Physiology and Pathology.Current issues in molecular biology · 2024Review
- Whole-genome duplication in an algal symbiont bolsters coral heat tolerance.Science advances · 2024Article
- Evolutionary screening of precision oncology biomarkers and its applications in prognostic model construction.iScience · 2024Article
- Fbrsl1 is required for heart development in Xenopus laevis and de novo variants in FBRSL1 can cause human heart defects.Disease models & mechanisms · 2024Article
- Essentiality, protein-protein interactions and evolutionary properties are key predictors for identifying cancer-associated genes using machine learning.Scientific reports · 2024Article
- Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes.Journal of molecular evolution · 2023Article
- Lost and Found: The Family of NF-κB Inhibitors Is Larger than Assumed in Salmonid Fish.International journal of molecular sciences · 2023Article
- Review
- Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.
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