ArticleNature ecology & evolution2023
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.
Article in Nature ecology & evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 57 citations in OpenAlex.
- Ancient enzymes, new biotechnology applications.Nature reviews. Molecular cell biology · 2026Article
- Chromosome-level Streptochaeta genome elucidates the ancestral karyotype and allopolyploid origin of grasses.Nature communications · 2026Article
- The evolution of structural variation across 500 million years of vertebrate evolution.bioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- A near telomere-to-telomere genome assembly of the Amur stickleback (Zoological research · 2026Article
- Species-rich and genomically diverse: comparative genomics reveals how fusions, fissions, and sex chromosomes have shaped beetle evolution.bioRxiv : the preprint server for biology · 2026Article
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- PGDD 2.0: Plant Genome Duplication Database with updated content and tools.Nucleic acids research · 2026Article
- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- High-quality chromosome-level genome assembly of the snake Pseudoxenodon stejnegeri (Squamata: Colubridae).Scientific data · 2025Article
- Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Genome architecture evolution in an invasive copepod species complex.Nature communications · 2025Article
- Zebrafish fast muscle contractions avoid the mammalian requirement for voltage-gated Na+ channels.PLoS biology · 2025Article
- Random, fragile, or correlated: Mechanisms of synteny decay in mammals.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
- EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.Nature ecology & evolution · 2025Article
- The Primate Major Histocompatibility Complex: A Case Study of Gene Family Evolution.bioRxiv : the preprint server for biology · 2025Article
- Article
- EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.NAR genomics and bioinformatics · 2025Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organizations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organizations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal gene order reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and interchromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.
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