ArticleGenome research2006
Reconstructing contiguous regions of an ancestral genome.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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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.
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Who cites it
117 citing papers in PubMed, 300 citations in OpenAlex.
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Random, fragile, or correlated: Mechanisms of synteny decay in mammals.bioRxiv : the preprint server for biology · 2025Article
- EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.Nature ecology & evolution · 2025Article
- Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats.Nature ecology & evolution · 2025Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- A chromosome-level genome assembly of the Korean minipig (Sus scrofa).Scientific data · 2024Article
- Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.BMC genomics · 2024Article
- AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa).Scientific data · 2023Article
- Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.Nature ecology & evolution · 2023Article
- Reference-based read clustering improves theComputational and structural biotechnology journal · 2023Article
- Evolution of the ancestral mammalian karyotype and syntenic regions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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- OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.Nucleic acids research · 2021Article
- A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.GigaScience · 2021Article
- Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.Ecology and evolution · 2020Article
- Review
- Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies.Molecular biology and evolution · 2020Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. We identify 3171 intervals, covering approximately 92% of the human genome, within which we find no rearrangements larger than 50 kilobases (kb) in the lineages leading to human, mouse, rat, and dog from their most recent common ancestor. Combining intervals that are adjacent in all contemporary species produces 1338 segments that may contain large insertions or deletions but that are free of chromosome fissions or fusions as well as inversions or translocations >50 kb in length. We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals.
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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.