ArticleGenome research2004
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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.
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.
Who cites it
103 citing papers in PubMed, 240 citations in OpenAlex.
- 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
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- The rate and spectrum of new mutations in mice inferred by long-read sequencing.Genome research · 2025Article
- De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes.Genome research · 2024Article
- Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants.Algorithms for molecular biology : AMB · 2024Article
- Evolution of the ancestral mammalian karyotype and syntenic regions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans.Cell reports · 2022Article
- Molecular Composition of Heterochromatin and Its Contribution to Chromosome Variation in theGenes · 2021Article
- More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs).Molecular biology and evolution · 2020Article
- Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer.Genome biology and evolution · 2020Article
- Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha.Molecular biology and evolution · 2019Article
- A novel approach to differentiate rat embryonic stem cells in vitro reveals a role for RNF12 in activation of X chromosome inactivation.Scientific reports · 2019Article
- Article
- Identification of two independent X-autosome translocations in closely related mammalian (Proechimys) species.Scientific reports · 2019Article
- Resolution effects in reconstructing ancestral genomes.BMC genomics · 2018Article
- A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians.PloS one · 2018Article
- The impact of the protein interactome on the syntenic structure of mammalian genomes.PloS one · 2017Article
- Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.Genome biology and evolution · 2016Article
- Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.BMC bioinformatics · 2016Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent analysis of genome rearrangements in human and mouse genomes revealed evidence for more rearrangements than thought previously and shed light on previously unknown features of mammalian evolution, like breakpoint reuse and numerous microrearrangements. However, two-way analysis cannot reveal the genomic architecture of ancestral mammals or assign rearrangement events to different lineages. Thus, the "original synteny" problem introduced by Nadeau and Sankoff previously, remains unsolved, as at least three mammalian genomes are required to derive the ancestral mammalian karyotype. We show that availability of the rat genome allows one to reconstruct a putative genomic architecture of the ancestral murid rodent genome. This reconstruction suggests that this ancestral genome retained many previously postulated chromosome associations in the placental ancestor and reveals others that were beyond the resolution of cytogenetic, radiation hybrid mapping, and chromosome painting techniques. Three-way analysis of rearrangements leads to a reliable reconstruction of the genomic architecture of specific regions in the murid ancestor, including the X chromosome, and for the first time allows one to assign major rearrangement events to one of human, mouse, and rat lineages. Our analysis implies that the rate of rearrangements is much higher in murid rodents than in the human lineage and confirms the existence of rearrangement hot-spots in all three lineages.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.