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Evaluation of results using simulated and real genome assemblies indicates that our approach can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available. We used RACA to reconstruct 60 Tibetan antelope (\n            <jats:italic>Pantholops hodgsonii<\/jats:italic>\n            ) chromosome fragments from 1,434 SOAPdenovo sequence scaffolds, of which 16 chromosome fragments were homologous to complete cattle chromosomes. Experimental validation by PCR showed that predictions made by RACA are highly accurate. Our results indicate that RACA will significantly facilitate the study of chromosome evolution and genome rearrangements for the large number of genomes being sequenced by NGS that do not have a genetic or physical map.\n          <\/jats:p>","DOI":"10.1073\/pnas.1220349110","type":"journal-article","created":{"date-parts":[[2013,1,11]],"date-time":"2013-01-11T05:09:12Z","timestamp":1357880952000},"page":"1785-1790","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":121,"title":["Reference-assisted chromosome assembly"],"prefix":"10.1073","volume":"110","author":[{"given":"Jaebum","family":"Kim","sequence":"first","affiliation":[{"name":"Institute for Genomic Biology, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801;"},{"name":"Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Korea;"}]},{"given":"Denis M.","family":"Larkin","sequence":"additional","affiliation":[{"name":"Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, United Kingdom;"}]},{"given":"Qingle","family":"Cai","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute, Shenzhen 518083, China;"}]},{"family":"Asan","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute, Shenzhen 518083, China;"}]},{"given":"Yongfen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute, Shenzhen 518083, China;"}]},{"given":"Ri-Li","family":"Ge","sequence":"additional","affiliation":[{"name":"Key Laboratory for High Altitude Medicine, Ministry of Chinese Education and Research Center for High Altitude Medicine, Qinghai University, Xining, Qinghai 810001, China;"}]},{"given":"Loretta","family":"Auvil","sequence":"additional","affiliation":[{"name":"National Center for Supercomputing Applications, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801;"},{"name":"Illinois Informatics Institute, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61802;"}]},{"given":"Boris","family":"Capitanu","sequence":"additional","affiliation":[{"name":"National Center for Supercomputing Applications, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801;"},{"name":"Illinois Informatics Institute, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61802;"}]},{"given":"Guojie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute, Shenzhen 518083, China;"}]},{"given":"Harris A.","family":"Lewin","sequence":"additional","affiliation":[{"name":"Institute for Genomic Biology, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801;"},{"name":"Department of Evolution and Ecology, University of California, Davis, CA 95616; and"}]},{"given":"Jian","family":"Ma","sequence":"additional","affiliation":[{"name":"Institute for Genomic Biology, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801;"},{"name":"Department of Bioengineering, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61801"}]}],"member":"341","published-online":{"date-parts":[[2013,1,10]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0168-9525(00)02081-3","article-title":"Conserved noncoding sequences are reliable guides to regulatory elements","volume":"16","author":"Hardison RC","year":"2000","unstructured":"RC Hardison, Conserved noncoding sequences are reliable guides to regulatory elements. 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Genome Res 18, 821\u2013829 (2008).","journal-title":"Genome Res"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase Update, a database of eukaryotic repetitive elements","volume":"110","author":"Jurka J","year":"2005","unstructured":"J Jurka, et al., Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110, 462\u2013467 (2005).","journal-title":"Cytogenet Genome Res"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.ygeno.2010.03.001","article-title":"Assembly algorithms for next-generation sequencing data","volume":"95","author":"Miller JR","year":"2010","unstructured":"JR Miller, S Koren, G Sutton, Assembly algorithms for next-generation sequencing data. 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(2010)."},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1101\/gr.131383.111","article-title":"GAGE: A critical evaluation of genome assemblies and assembly algorithms","volume":"22","author":"Salzberg SL","year":"2012","unstructured":"SL Salzberg, et al., GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res 22, 557\u2013567 (2012).","journal-title":"Genome Res"},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1126\/science.1169588","article-title":"The genome sequence of taurine cattle: A window to ruminant biology and evolution","volume":"324","author":"Elsik CG","year":"2009","unstructured":"CG Elsik, et al., The genome sequence of taurine cattle: A window to ruminant biology and evolution. 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Genome Res 19, 943\u2013957 (2009).","journal-title":"Genome Res"},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1089\/cmb.2008.0069","article-title":"DUPCAR: Reconstructing contiguous ancestral regions with duplications","volume":"15","author":"Ma J","year":"2008","unstructured":"J Ma, et al., DUPCAR: Reconstructing contiguous ancestral regions with duplications. J Comput Biol 15, 1007\u20131027 (2008).","journal-title":"J Comput Biol"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li H","year":"2009","unstructured":"H Li, R Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1101\/gr.086546.108","article-title":"Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories","volume":"19","author":"Larkin DM","year":"2009","unstructured":"DM Larkin, et al., Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res 19, 770\u2013777 (2009).","journal-title":"Genome Res"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent WJ","year":"2002","unstructured":"WJ Kent, et al., The human genome browser at UCSC. 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