ArticleBMC bioinformatics2011
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- The application of irreversible genomic states to define and trace ancient cell type homologies.EvoDevo · 2025Article
- Phylogeny and Functional Differentiation of the Terpene Synthase Gene Family in Angiosperms with Emphasis onInternational journal of molecular sciences · 2025Article
- Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions.BMC genomics · 2022Article
- Deeply conserved synteny and the evolution of metazoan chromosomes.Science advances · 2022Article
- Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution.Nature communications · 2021Article
- Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns.The Plant journal : for cell and molecular biology · 2020Article
- Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases inBiomolecules · 2019Article
- Reply to Nakatani and McLysaght: Analyzing deep duplication events.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation.The Plant cell · 2017Article
- Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.GigaScience · 2014Article
- Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.Genome research · 2012Article
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3 authors.
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Abstract
backgroundMany metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation.
resultsWe examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c.
conclusionsA simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
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