ArticleGenome research2009
Recovering genome rearrangements in the mammalian phylogeny.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Local Genomic Instability of theGenes · 2024Article
- Review
- Review
- A New Algorithm for Identifying Genome Rearrangements in the Mammalian Evolution.Frontiers in genetics · 2019Article
- Banding cytogenetics of chimeric hybridsComparative cytogenetics · 2018Article
- Banding cytogenetics of the Barbary partridgeComparative cytogenetics · 2018Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.Genome biology and evolution · 2016Article
- Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease.Chromosoma · 2016Review
- Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis).BMC genomics · 2015Article
- ProCARs: Progressive Reconstruction of Ancestral Gene Orders.BMC genomics · 2015Article
- Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens.BMC genomics · 2014Article
- A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.Molecular ecology · 2014Article
- Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.BMC genomics · 2014Article
- Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions.BMC genomics · 2014Article
- The precarious prokaryotic chromosome.Journal of bacteriology · 2014Review
- Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.PloS one · 2014Article
- What is the difference between the breakpoint graph and the de Bruijn graph?BMC genomics · 2014Article
- Nonspaced inverted DNA repeats are preferential targets for homology-directed gene repair in mammalian cells.Nucleic acids research · 2012Article
- Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of genome rearrangements provides a global view on the evolution of a set of related species. We present a new algorithm called EMRAE (efficient method to recover ancestral events) to reliably predict a wide-range of rearrangement events in the ancestry of a group of species. Using simulated data sets, we show that EMRAE achieves comparable sensitivity but significantly higher specificity when predicting evolutionary events relative to other tools to study genome rearrangements. We apply our approach to the synteny blocks of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog) and predict 1109 rearrangement events, including 831 inversions, 15 translocations, 237 transpositions, and 26 fusions/fissions. Studying the sequence features at the breakpoints of the primate rearrangement events, we demonstrate that they are not only enriched in segmental duplications (SDs), but that the enrichment of matching pairs of SDs is even stronger within the pairs of breakpoints associated with recovered events. We also show that pairs of L1 repeats are frequently associated with ancestral inversions across all studied lineages. Together, this substantiates the model that regions of high sequence identity have been associated with rearrangement events throughout the mammalian phylogeny.
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