10.1101/gr.5383506Access the most recent version at doi: published online Sep 18, 2006; Genome Res. Blanchette, David Haussler and Webb Miller Jian Ma, Louxin Zhang, Bernard B. Suh, Brian J. Raney, Richard C. Burhans, W. James Kent, Mathieu Reconstructing contiguous regions of an ancestral genome dataSupplementary http://www.genome.org/cgi/content/full/gr.5383506/DC1 "Supplemental Research Data" P<PPublished online September 18, 2006 in advance of the print journal. Open AccessFreely available online through the Genome Research Open Access option. serviceEmail alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the Notes object identifier (DOIs) and date of initial publication. by PubMed from initial publication. Citations to Advance online articles must include the digital publication). Advance online articles are citable and establish publication priority; they are indexedappeared in the paper journal (edited, typeset versions may be posted when available prior to final Advance online articles have been peer reviewed and accepted for publication but have not yet http://www.genome.org/subscriptions/ go to: Genome ResearchTo subscribe to © 2006 Cold Spring Harbor Laboratory Press on October 31, 2006 www.genome.orgDownloaded fromReconstructing contiguous regionsof an ancestral genomeJian Ma,1,5,6Louxin Zhang,2Bernard B. Suh,3Brian J. Raney,3Richard C. Burhans,1W. James Kent,3Mathieu Blanchette,4David Haussler,3and Webb Miller11Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA;2Department of Mathematics, National University of Singapore, Singapore 117543;3Center for Biomolecular Science andEngineering, University of California Santa Cruz, Santa Cruz, California 95064, USA;4School of Computer Science, McGillUniversity, Montreal, Quebec H3A 2B4, CanadaThis article analyzes mammalian genome rearrangements at higher resolution than has been published to date. Weidentify 3171 intervals, covering ∼92% of the human genome, within which we find no rearrangements larger than 50kilobases (kb) in the lineages leading to human, mouse, rat, and dog from their most recent common ancestor.Combining intervals that are adjacent in all contemporary species produces 1338 segments that may contain largeinsertions or deletions but that are free of chromosome fissions or fusions as well as inversions or translocations >50kb in length. We describe a new method for predicting the ancestral order and orientation of those intervals fromtheir observed adjacencies in modern species. We combine the results from this method with data from chromosomepainting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the availablehuman genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysisof the predicted evolutionary breakpoints in the human lineage confirms certain published observations butdisagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, ourtheoretical analyses and computer simulations indicate that our results are reasonably accurate and that they willbecome highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstructthe genome sequence of the last ancestor of human, dogs, and most other placental mammals.[Supplemental material is available online at www.genome.org and http://www.bx.psu.edu/miller_lab/.]Using computer simulations, we have shown (Blanchette et al.2004) that the genome sequence of the so-called Boreoeutherianancestor (Fig. 1) can be computationally predicted at high accu-racy within most euchromatic intervals that are free of large-scalerearrangements, given adequate data from living mammals. Forinstance, when sequences from 20 appropriately chosen mam-malian species are available, we expect that >98% of the recon-structed nucleotides will be identical to the corresponding ances-tral base. Because all mammals have experienced large-scale ge-nomic rearrangements since their last common ancestor, in orderto determine regional correspondence we analyze these rear-rangements to infer a partition of each genome into intervalswhere nucleotide-level reconstruction methods can be applied.The regional correspondence between modern and ancestralchromosomes has been predicted with increasing accuracy by anumber of groups using a variety of methods. Currently, themain experimental technique is chromosomal painting (for sur-veys, see Wienberg 2004 and Froenicke et al. 2006), in whichfluorescently labeled chromosomes from one species are hybrid-ized to chromosomes from another species. Although the re-quirement of optical visibility means that the cytogenetic ap-proach can recognize only rearrangements with conserved seg-ments longer than 4 Mb (Froenicke et al. 2006) and cannotidentify intrachromosomal rearrangements (Wienberg 2004), thechromosomal painting approach has the advantage that data areavailable for over 80 mammals (50 primates). Alternatively, com-putational methods that attempt to identify orthologous ge-nomic intervals have much higher resolution, potentially downto under a kilobase. However, only a handful of vertebrate ge-nomes are currently sequenced with sufficient precision andcompleteness to be informative for such an analysis. Using acombination of these two approaches, Murphy et al. (2005) es-timated the rearrangement rates in the lineages leading to hu-man, mouse, rat, cat, cattle, dog, pig, and horse, and predictedthat the Boreoeutherian ancestor had 24 chromosomes.To predict large-scale relationships among modern and an-cestral genomes with sufficient accuracy for our needs, we havedevised new methods. Conserved genomic segments are identi-fied directly from freely available data and analyzed by a newcomputer program, as described below. We also estimate the ac-curacy of our results, compare them with published analyses, andexplore the biological properties of rearrangement sites. Thecomputer software described herein and details of our predic-tions for human, mouse, rat, and dog are freely available athttp://www.bx.psu.edu/miller_lab/.ResultsSegmenting the genomes based on pair-wise alignmentsTo predict segments of the ancestral genome, we start with “nets”(Kent et al. 2003), downloaded from the UCSC Human GenomeBrowser
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