{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T20:47:21Z","timestamp":1762375641628},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Fractionation is arguably the greatest cause of gene order disruption following whole genome duplication, causing severe biases in chromosome rearrangement-based estimates of evolutionary divergence.<\/jats:p>\n               <jats:p>Results: We show how to correct for this bias almost entirely by means of a \u2018consolidation\u2019 algorithm for detecting and suitably transforming identifiable regions of fractionation. We characterize the process of fractionation and the performance of the algorithm through realistic simulations. We apply our method to a number of core eudicot genomes, we and by studying the fractionation regions detected, are able to address topical issues in polyploid evolution.<\/jats:p>\n               <jats:p>Availability and implementation: Code for the consolidation algorithm, and sample data, is available at: http:\/\/137.122.149.195\/Software\/Fractionation\/fractionation.html<\/jats:p>\n               <jats:p>Contact: \u00a0sankoff@uottawa.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts392","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i402-i408","source":"Crossref","is-referenced-by-count":22,"title":["Fractionation, rearrangement and subgenome dominance"],"prefix":"10.1093","volume":"28","author":[{"given":"David","family":"Sankoff","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5"}]},{"given":"Chunfang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513050943900_B1","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/ng.736","article-title":"The genome of Theobroma cacao.","volume":"43","author":"Argout","year":"2001","journal-title":"Nat. Genet."},{"key":"2023012513050943900_B2","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1126\/science.1095781","article-title":"The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome","volume":"304","author":"Dietrich","year":"2004","journal-title":"Science"},{"key":"2023012513050943900_B3","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.2307\/3871311","article-title":"A sense of self: the role of DNA sequence elimination in allopolyploidization","volume":"13","author":"Eckardt","year":"2001","journal-title":"Plant Cell"},{"key":"2023012513050943900_B4","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/978-1-61779-582-4_15","article-title":"Analysis of gene order evolution beyond single-copy genes","volume-title":"Evolutionary Genomics","author":"El-Mabrouk","year":"2012"},{"key":"2023012513050943900_B5","volume-title":"Combinatorics of Genome Rearrangements","author":"Fertin","year":"1974"},{"key":"2023012513050943900_B6","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.pbi.2012.01.015","article-title":"Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants","volume":"15","author":"Freeling","year":"2012","journal-title":"Curr. Opin. Plant Biol."},{"key":"2023012513050943900_B7","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/nature06148","article-title":"The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla","volume":"449","author":"Jaillon","year":"2007","journal-title":"Nature"},{"key":"2023012513050943900_B8","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nature02424","article-title":"Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae","volume":"428","author":"Kellis","year":"2004","journal-title":"Nature"},{"key":"2023012513050943900_B9","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1093\/genetics\/166.2.935","article-title":"Genomic duplication, fractionation and the origin of regulatory novelty","volume":"166","author":"Langham","year":"2004","journal-title":"Genetics"},{"key":"2023012513050943900_B10","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1111\/j.1365-313X.2007.03326.x","article-title":"How to usefully compare homologous plant genes and chromosomes as DNA sequences","volume":"53","author":"Lyons","year":"2008","journal-title":"Plant J."},{"key":"2023012513050943900_B11","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1104\/pp.108.124867","article-title":"Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids","volume":"148","author":"Lyons","year":"2008","journal-title":"Plant Physiol."},{"key":"2023012513050943900_B12","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.tcs.2004.02.039","article-title":"Genomic distances under deletions and insertions","volume":"325","author":"Marron","year":"2004","journal-title":"Theor. Compu. Sci."},{"key":"2023012513050943900_B13","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1093\/bioinformatics\/15.11.909","article-title":"Genome rearrangement with gene families","volume":"15","author":"Sankoff","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012513050943900_B14","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1089\/cmb.2009.0103","article-title":"Towards improved reconstruction of ancestral gene order in angiosperm phylogeny","volume":"16","author":"Sankoff","year":"2009","journal-title":"J. Comput. Biol."},{"key":"2023012513050943900_B15","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1073\/pnas.1101368108","article-title":"Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss","volume":"108","author":"Schnable","year":"2011","journal-title":"Proc. Nat. Acad. Sci. USA."},{"key":"2023012513050943900_B16","doi-asserted-by":"crossref","first-page":"336","DOI":"10.3732\/ajb.0800079","article-title":"Polyploidy and angiosperm diversification","volume":"96","author":"Soltis","year":"2009","journal-title":"Am. J. Botany"},{"key":"2023012513050943900_B17","first-page":"1596","article-title":"The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)","volume":"313","author":"Tuskan","year":"2006","journal-title":"Science 2006"},{"key":"2023012513050943900_B18","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1101\/gr.107284.110","article-title":"Patching gaps in plant genomes results in gene movement and erosion of colinearity","volume":"20","author":"Wicker","year":"2010","journal-title":"Genome Res."},{"key":"2023012513050943900_B19","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/42711","article-title":"Molecular evidence for an ancient duplication of the entire yeast genome","volume":"387","author":"Wolfe","year":"1997","journal-title":"Nature"},{"key":"2023012513050943900_B20","first-page":"4241","article-title":"Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the Rosids","volume":"23","author":"Woodhouse","year":"2011","journal-title":"Plant Cell 2011"},{"key":"2023012513050943900_B21","first-page":"295","article-title":"Genome halving with an outgroup","volume":"2","author":"Zheng","year":"2007","journal-title":"Evol. Bioinformatics Online"},{"key":"2023012513050943900_B22","doi-asserted-by":"crossref","first-page":"i96","DOI":"10.1093\/bioinformatics\/btn146","article-title":"Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes","volume":"24","author":"Zheng","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012513050943900_B23","article-title":"Ancient angiosperm hexaploidy meets gene order reconstruction of the eudicot ancestor","volume-title":"Second IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","author":"Zheng","year":"2012"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/18\/i402\/48885144\/bioinformatics_28_18_i402.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/18\/i402\/48885144\/bioinformatics_28_18_i402.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:56:39Z","timestamp":1674672999000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/18\/i402\/247278"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,3]]},"references-count":23,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2012,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts392","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,9,15]]},"published":{"date-parts":[[2012,9,3]]}}}