<i>De Novo</i> Gene Emergence: Summary, Classification, and Challenges of Current Methods

A novel mechanism of de novo gene origination from nongenic sequences was first proposed in the early 2000s. Subsequent studies have since provided evidence of de novo gene emergence across all domains of life, revealing its occurrence to be more frequent than initially anticipated. While studies mainly agree on the general concept of de novo emergence from nongenic DNA, the exact methods and definitions for detecting de novo genes differ significantly. Here, we provide a comprehensive step-by-step description of the most commonly used methods for de novo gene detection. In addition, we address the limitations of nomenclature and detection methods and clarify some complex concepts that are sometimes misused. This review is accompanied by the publication of a de novo gene annotation format to standardize the reporting of methodology, enable reproducibility and improve the comparability of datasets.

Authors

Institutions

Publication Details

Journal
Genome Biology and Evolution
Published
2025-10-21
DOI
https://doi.org/10.1093/gbe/evaf197
Citations
3
Primary Topic
Genetics, Bioinformatics, and Biomedical Research
Type
article
Field-Weighted Citation Impact
2.42
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods

Anna Grandchamp, Victor Luria, Paul Roginski, Amir Karger et al.
3 citations
Genome Biology and Evolution
Genetics, Bioinformatics, and Biomedical Research
2.42
article

De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods

Anna Grandchamp, Victor Luria, Paul Roginski, Amir Karger, Elias Dohmen, Lars A. Eicholt, Margaux Aubel
article en
3 citations

Abstract

A novel mechanism of de novo gene origination from nongenic sequences was first proposed in the early 2000s. Subsequent studies have since provided evidence of de novo gene emergence across all domains of life, revealing its occurrence to be more frequent than initially anticipated. While studies mainly agree on the general concept of de novo emergence from nongenic DNA, the exact methods and definitions for detecting de novo genes differ significantly. Here, we provide a comprehensive step-by-step description of the most commonly used methods for de novo gene detection. In addition, we address the limitations of nomenclature and detection methods and clarify some complex concepts that are sometimes misused. This review is accompanied by the publication of a de novo gene annotation format to standardize the reporting of methodology, enable reproducibility and improve the comparability of datasets.

Genome Biology and EvolutionVol. 17(11)
Boston Children's Hospital (US), Centre National de la Recherche Scientifique (FR), Harvard University (US), Inserm (FR), Aix-Marseille Université (FR), University of Münster (DE), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Yale University (US), Institute for Biodiversity (DE), Institut de Biologie Intégrative de la Cellule (FR), Theories and Approaches of Genomic Complexity (FR), CEA Paris-Saclay (FR), Center for Systems Biology (US)
Openalex Percentile: Top 10%
Genetics, Bioinformatics, and Biomedical Research
2.42
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.