{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T22:02:05Z","timestamp":1704924125044},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"S19","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n It has recently been shown that fractionation, the random loss of excess gene copies after a whole genome duplication event, is a major cause of gene order disruption. When estimating evolutionary distances between genomes based on chromosomal rearrangement, fractionation inevitably leads to significant overestimation of classic rearrangement distances. This bias can be largely avoided when genomes are preprocessed by \"consolidation\", a procedure that identifies and accounts for regions of fractionation.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n In this paper, we present a new consolidation algorithm that extends and improves previous work in several directions. We extend the notion of the fractionation region to use information provided by regions where this process is still ongoing. The new algorithm can optionally work with this new definition of fractionation region and is able to process not only tetraploids but also genomes that have undergone hexaploidization and polyploidization events of higher order. Finally, this algorithm reduces the asymptotic time complexity of consolidation from quadratic to linear dependence on the genome size. The new algorithm is applied both to plant genomes and to simulated data to study the effect of fractionation in ancient hexaploids.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2105-13-s19-s8","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T01:59:39Z","timestamp":1576029579000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["A consolidation algorithm for genomes fractionated after higher order polyploidization"],"prefix":"10.1186","volume":"13","author":[{"given":"Katharina","family":"Jahn","sequence":"first","affiliation":[]},{"given":"Chunfang","family":"Zheng","sequence":"additional","affiliation":[]},{"given":"Jakub","family":"Kov\u00e1\u010d","sequence":"additional","affiliation":[]},{"given":"David","family":"Sankoff","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,12,19]]},"reference":[{"key":"5517_CR1","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1534\/genetics.166.2.935","volume":"166","author":"R Langham","year":"2004","unstructured":"Langham R, Walsh J, Dunn M, Ko C, Goff SA, Freeling M: Genomic duplication, fractionation and the origin of regulatory novelty. Genetics. 2004, 166: 935-945. 10.1534\/genetics.166.2.935.","journal-title":"Genetics"},{"key":"5517_CR2","doi-asserted-by":"publisher","first-page":"336","DOI":"10.3732\/ajb.0800079","volume":"96","author":"DE Soltis","year":"2009","unstructured":"Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS: Polyploidy and angiosperm diversification. American Journal of Botany. 2009, 96: 336-348. 10.3732\/ajb.0800079.","journal-title":"American Journal of Botany"},{"key":"5517_CR3","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.pbi.2012.01.015","volume":"15","author":"M Freeling","year":"2012","unstructured":"Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC: Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current Opinion in Plant Biology. 2012, 15: 131-139. 10.1016\/j.pbi.2012.01.015.","journal-title":"Current Opinion in Plant Biology"},{"key":"5517_CR4","doi-asserted-by":"publisher","first-page":"1699","DOI":"10.1105\/tpc.13.8.1699","volume":"13","author":"N Eckardt","year":"2001","unstructured":"Eckardt N: A sense of self: the role of DNA sequence elimination in allopoly-ploidization. Plant Cell. 2001, 13: 1699-1704.","journal-title":"Plant Cell"},{"key":"5517_CR5","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/42711","volume":"387","author":"KH Wolfe","year":"1997","unstructured":"Wolfe KH, Shields DC: Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997, 387: 708-713. 10.1038\/42711.","journal-title":"Nature"},{"key":"5517_CR6","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1126\/science.1095781","volume":"304","author":"FS Dietrich","year":"2004","unstructured":"Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, P\u00f6hlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P: The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004, 304: 304-307. 10.1126\/science.1095781.","journal-title":"Science"},{"key":"5517_CR7","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nature02424","volume":"428","author":"M Kellis","year":"2004","unstructured":"Kellis M, Birren BW, Lander ES: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004, 428: 617-624. 10.1038\/nature02424.","journal-title":"Nature"},{"key":"5517_CR8","volume-title":"Bioinformatics","author":"D Sankoff","year":"2012","unstructured":"Sankoff D, Zheng Z: Fractionation, rearrangement and subgenome dominance. Bioinformatics. 2012"},{"key":"5517_CR9","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/nature06148","volume":"449","author":"Ot Jaillon","year":"2007","unstructured":"Jaillon Ot: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007, 449: 463-467. 10.1038\/nature06148.","journal-title":"Nature"},{"key":"5517_CR10","unstructured":"Zheng C, Chen E, Albert VA, Lyons E, Sankoff D: Ancient eudicot hexaploidy meets ancestral eurosid gene order. submitted."},{"key":"5517_CR11","first-page":"88","volume-title":"Latin American Theoretical Informatics, Volume 1776 of LNCS","author":"MA Bender","year":"2000","unstructured":"Bender MA, Farach-Colton M: The LCA problem revisited. Latin American Theoretical Informatics, Volume 1776 of LNCS. 2000, Springer Verlag, 88-94."},{"key":"5517_CR12","first-page":"459","volume-title":"Proceedings of the 1st International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE'07), Volume 4614 of LNCS","author":"J Fischer","year":"2007","unstructured":"Fischer J, Heun V: A new succinct representation of RMQ-information and improvements in the enhanced suffix array. Proceedings of the 1st International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE'07), Volume 4614 of LNCS. 2007, 459-470."},{"key":"5517_CR13","volume-title":"Poster at SMBE (Society for Molecular Biology & Evolution)","author":"J Leebens-Mack","year":"2012","unstructured":"Leebens-Mack J, Der J, Ayyampalayam S, Burnett J, Chamala S, Chanderbali A, Estill J, Jiao Y, Liu K, Lan T, Lyons E, Tomsho L, Tang H, Wafula E, Walts B, Albert V, Barbazuk B, Ma H, Sankoff D, Schuster S, Soltis D, Soltis P, Wessler S, dePamphilis C: The Amborella genome: An evolutionary reference sequence for comparative plant genomics. Poster at SMBE (Society for Molecular Biology & Evolution). 2012"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S19-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S19-S8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S19-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T21:17:14Z","timestamp":1630531034000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S19-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12]]},"references-count":13,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5517"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s19-s8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12]]},"assertion":[{"value":"19 December 2012","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S8"}}