{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T20:00:03Z","timestamp":1776542403440,"version":"3.51.2"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S9","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Many metazoan genomes conserve chromosome-scale gene linkage relationships (\u201cmacro-synteny\u201d) from the common ancestor of multicellular animal life [1\u20134], 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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We 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 (\u201cDCJ-[C]\u201d), and is available as open source software from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/github.com\/putnamlab\/dcj-c\" ext-link-type=\"uri\">http:\/\/github.com\/putnamlab\/dcj-c<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>A 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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s9-s11","type":"journal-article","created":{"date-parts":[[2011,10,5]],"date-time":"2011-10-05T18:47:37Z","timestamp":1317840457000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes"],"prefix":"10.1186","volume":"12","author":[{"given":"Jie","family":"Lv","sequence":"first","affiliation":[]},{"given":"Paul","family":"Havlak","sequence":"additional","affiliation":[]},{"given":"Nicholas H","family":"Putnam","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,10,5]]},"reference":[{"issue":"5834","key":"4818_CR1","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1126\/science.1139158","volume":"317","author":"NH Putnam","year":"2007","unstructured":"Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS: Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. 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