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Abstract
The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.
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Khan AH, Zou Z, Xiang Y, Chen S, Tian XL. Conserved signaling pathways genetically associated with longevity across the species. Biochim Biophys Acta Mol Basis Dis 2018; 1865:1745-1755. [PMID: 31109448 DOI: 10.1016/j.bbadis.2018.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/26/2018] [Accepted: 09/04/2018] [Indexed: 02/08/2023]
Abstract
Advanced age is an independent risk factor for natural death and common diseases, such as cardiovascular diseases, dementia, and cancers, which are life-threatening and cause disabilities. On the other hand, individual with healthy longevity is a plausible model for successful aging. Thus, search for longevity-associated genes and pathways likely provides a unique approach to understand the genetic mechanisms underlying aging and healthspan, and emerging evidence from model organisms has highlighted the significance of genetic components in longevity. Here we reviewed the uses of model organisms including yeast, ciliate, nematode, arthropod, fish, rodent, and primate as well as human to identify the genetic determinants of longevity and discussed the genetic contributions of conserved longevity pathways, such as adrenergic system, AMPK, insulin/IGF-1, and mTOR signaling pathways.
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Affiliation(s)
- Abdul Haseeb Khan
- Human population genetics, Human Aging Research Institute (HARI), Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China; School of Life Science, Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China
| | - Zhiwen Zou
- School of Life Science, Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China
| | - Yang Xiang
- Human population genetics, Human Aging Research Institute (HARI), Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China; School of Life Science, Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China
| | - Shenghan Chen
- Human population genetics, Human Aging Research Institute (HARI), Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China; School of Life Science, Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China
| | - Xiao-Li Tian
- Human population genetics, Human Aging Research Institute (HARI), Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China; School of Life Science, Nanchang University, Xuefu Rd 999, Honggutan New District, Nanchang, Jiangxi Province 330031, China.
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3
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Bozdag S, Close TJ, Lonardi S. A graph-theoretical approach to the selection of the minimum tiling path from a physical map. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:352-360. [PMID: 23929859 DOI: 10.1109/tcbb.2013.26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The problem of computing the minimum tiling path (MTP) from a set of clones arranged in a physical map is a cornerstone of hierarchical (clone-by-clone) genome sequencing projects. We formulate this problem in a graph theoretical framework, and then solve by a combination of minimum hitting set and minimum spanning tree algorithms. The tool implementing this strategy, called FMTP, shows improved performance compared to the widely used software FPC. When we execute FMTP and FPC on the same physical map, the MTP produced by FMTP covers a higher portion of the genome, and uses a smaller number of clones. For instance, on the rice genome the MTP produced by our tool would reduce by about 11 percent the cost of a clone-by-clone sequencing project. Source code, benchmark data sets, and documentation of FMTP are freely available at >http://code.google.com/p/fingerprint-based-minimal-tiling-path/ under MIT license.
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Affiliation(s)
- Serdar Bozdag
- Department of Mathematics, Statistics and Computer Science, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, USA.
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4
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Song X, Goicoechea JL, Ammiraju JSS, Luo M, He R, Lin J, Lee SJ, Sisneros N, Watts T, Kudrna DA, Golser W, Ashley E, Collura K, Braidotti M, Yu Y, Matzkin LM, McAllister BF, Markow TA, Wing RA. The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research. Genetics 2011; 187:1023-30. [PMID: 21321134 PMCID: PMC3070512 DOI: 10.1534/genetics.111.126540] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 02/05/2011] [Indexed: 11/18/2022] Open
Abstract
The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.
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Affiliation(s)
- Xiang Song
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jose Luis Goicoechea
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jetty S. S. Ammiraju
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Meizhong Luo
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Ruifeng He
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jinke Lin
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - So-Jeong Lee
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Nicholas Sisneros
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Tom Watts
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - David A. Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Wolfgang Golser
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Elizabeth Ashley
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Kristi Collura
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Michele Braidotti
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Yeisoo Yu
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Luciano M. Matzkin
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Bryant F. McAllister
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Therese Ann Markow
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Rod A. Wing
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 and Department of Biology, University of Iowa, Iowa City, Iowa 52242
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5
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Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP. A multiway analysis for identifying high integrity bovine BACs. BMC Genomics 2009; 10:46. [PMID: 19166603 PMCID: PMC2660975 DOI: 10.1186/1471-2164-10-46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 01/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. RESULTS The location of each bovine BAC in the BAC fingerprint-based genome map and in the genome assembly were compared based on the reported BESs, and for a smaller number of BACs the full sequence. BACs with consistent positions in all three datasets, or if the full sequence was not available, for both the fingerprint map and BES-based alignments, were deemed to be correctly positioned. BACs with consistent BES-based and fingerprint-based locations, but with conflicting locations based on the fully sequenced BAC, appeared to have been misidentified during sequencing, and included a number of apparently swapped BACs. Inconsistencies between BES-based and fingerprint map positions identified thirty one plates from the CHORI-240 library that appear to have suffered substantial systematic problems during the end-sequencing of the BACs. No systematic problems were identified in the fingerprinting of the BACs. Analysis of BACs overlapping in the assembly identified a small overrepresentation of clones with substantial overlap in the library and a substantial enrichment of highly overlapping BACs on the same plate in the CHORI-240 library. More than half of these BACs appear to have been present as duplicates on the original BAC-library plates and thus should be avoided in subsequent projects. CONCLUSION Our analysis shows that approximately 95% of the bovine CHORI-240 library clones with both a BAC fingerprint and two BESs mapping to the genome in the expected orientations (approximately 27% of all BACs) have consistent locations in the BAC fingerprint map and the genome assembly. We have developed a broadly applicable methodology for checking the integrity of BAC-based datasets even where only incomplete and partially assembled genomic sequence is available.
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Affiliation(s)
- Abhirami Ratnakumar
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, QLD 4067, Australia.
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6
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Mathewson CA, Schein JE, Marra MA. Large-scale BAC clone restriction digest fingerprinting. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.19. [PMID: 18428413 DOI: 10.1002/0471142905.hg0519s53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Restriction digest fingerprinting is a common method for characterizing large insert genomic clones, e.g., bacterial artificial chromosome (BAC), P1 artificial chromosome (PAC) and Fosmid clones. This clone fingerprinting method has been widely applied in the construction of clone-based physical maps, which have been used as positional cloning resources as well as to support directed and genome-wide sequencing efforts. This unit describes a robust, large-scale procedure for generation of agarose gel-based clone fingerprints from BAC clones.
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Affiliation(s)
- Carrie A Mathewson
- Canada's Michael Smith Genome Sciences Center Vancouver, British Columbia, Canada
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7
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Krzywinski M, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui A, Jones S, Schein J, Collins C, Marra M. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol 2008; 8:R224. [PMID: 17953769 PMCID: PMC2246298 DOI: 10.1186/gb-2007-8-10-r224] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 08/28/2007] [Accepted: 10/22/2007] [Indexed: 11/10/2022] Open
Abstract
Fingerprint Profiling (FPP) is a new method which uses restriction digest fingerprints of bacterial artificial chromosome (BAC) clones for detecting and classifying rearrangements in the human genome. We present a method, called fingerprint profiling (FPP), that uses restriction digest fingerprints of bacterial artificial chromosome clones to detect and classify rearrangements in the human genome. The approach uses alignment of experimental fingerprint patterns to in silico digests of the sequence assembly and is capable of detecting micro-deletions (1-5 kb) and balanced rearrangements. Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements.
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Affiliation(s)
- Martin Krzywinski
- BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6.
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8
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Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol 2008; 8:R165. [PMID: 17697342 PMCID: PMC2374996 DOI: 10.1186/gb-2007-8-8-r165] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/20/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly. Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
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Affiliation(s)
- Warren M Snelling
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jacqueline E Schein
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Matthew Hobbs
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | | | | | - Jan Aerts
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Gary L Bennett
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Ian E Bosdet
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Mekki Boussaha
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Alexandre R Caetano
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | - Marcos M Costa
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | | | - Brian P Dalrymple
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | - André Eggen
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Sandrine Floriot
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Mathieu Gautier
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Clare A Gill
- Texas A&M University, College Station, TX 77843, USA
| | - Ronnie D Green
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - Robert Holt
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Oliver Jann
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Steven JM Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven M Kappes
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - John W Keele
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Pieter J de Jong
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Denis M Larkin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Harris A Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Stephanie McKay
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Carrie A Mathewson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Stephen S Moore
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Brenda Murdoch
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Frank W Nicholas
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Kazutoyo Osoegawa
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Alice Roy
- Genoscope, rue Gaston Cremieux, 91057 Evry, France
| | - Hanni Salih
- Texas A&M University, College Station, TX 77843, USA
| | - Laurent Schibler
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Robert D Schnabel
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Licia Silveri
- Istituto di Zootecnica Università Cattolica del S Cuore, via E Parmense, 84 29100 Piacenza, Italy
| | - Loren C Skow
- Texas A&M University, College Station, TX 77843, USA
| | - Timothy PL Smith
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Tad S Sonstegard
- USDA, ARS, BARC Bovine Functional Genomics Laboratory, Maryland, USA
| | - Jeremy F Taylor
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ross Tellam
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | | | - John L Williams
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
- Current address: Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi 26900, Italy
| | | | - Natasja H Wye
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - George Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Shaying Zhao
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Current address: Department of Biochemistry and Molecular Biology, University of Georgia, Green Street, Athens, GA 30602-7229, USA
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9
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Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M, Sehra H, Yang F, Rogatcheva MB, Milan D, Chardon P, Rohrer G, Nonneman D, de Jong P, Meyers SN, Archibald A, Beever JE, Schook LB, Rogers J. A high utility integrated map of the pig genome. Genome Biol 2008; 8:R139. [PMID: 17625002 PMCID: PMC2323232 DOI: 10.1186/gb-2007-8-7-r139] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 06/21/2007] [Accepted: 07/11/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction. RESULTS Here we report the construction of the most highly continuous bacterial artificial chromosome (BAC) map of any mammalian genome, for the pig (Sus scrofa domestica) genome. The map provides a template for the generation and assembly of high-quality anchored sequence across the genome. The physical map integrates previous landmark maps with restriction fingerprints and BAC end sequences from over 260,000 BACs derived from 4 BAC libraries and takes advantage of alignments to the human genome to improve the continuity and local ordering of the clone contigs. We estimate that over 98% of the euchromatin of the 18 pig autosomes and the X chromosome along with localized coverage on Y is represented in 172 contigs, with chromosome 13 (218 Mb) represented by a single contig. The map is accessible through pre-Ensembl, where links to marker and sequence data can be found. CONCLUSION The map will enable immediate electronic positional cloning of genes, benefiting the pig research community and further facilitating use of the pig as an alternative animal model for human disease. The clone map and BAC end sequence data can also help to support the assembly of maps and genome sequences of other artiodactyls.
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Affiliation(s)
- Sean J Humphray
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Carol E Scott
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Richard Clark
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Brandy Marron
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Clare Bender
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Nick Camm
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Jayne Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Andrew Jenks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Angela Noon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Manish Patel
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Harminder Sehra
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Margarita B Rogatcheva
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Denis Milan
- Laboratoire de Génétique Cellulaire, INRA, 31326 Castanet-Tolosan, France
| | - Patrick Chardon
- INRA-CEA, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
| | - Gary Rohrer
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Dan Nonneman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Pieter de Jong
- Children's Hospital Oakland-BACPAC Resources, Oakland, California 94609, USA
| | - Stacey N Meyers
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | | | - Jonathan E Beever
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Lawrence B Schook
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Jane Rogers
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
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10
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Abstract
The rat genome project and the resources that it has generated are transforming the translation of rat biology to human medicine. The rat genome was sequenced to a high quality “draft,” the structure and location of the genes were predicted, and a global assessment was published (Gibbs RA et al., Nature 428: 493–521, 2004). Since that time, researchers have made use of the genome sequence and annotations and related resources. We take this opportunity to review the currently available rat genome resources and to discuss the progress and future plans for the rat genome.
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Affiliation(s)
- K. C. Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - G. M. Weinstock
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - R. A. Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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11
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Wu X, Zhong G, Findley SD, Cregan P, Stacey G, Nguyen HT. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map. BMC Genomics 2008; 9:28. [PMID: 18211698 PMCID: PMC2259328 DOI: 10.1186/1471-2164-9-28] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 01/22/2008] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. RESULTS A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (approximately 1x genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. CONCLUSION We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions in the genome, as well as for extending physical map contigs.
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Affiliation(s)
- Xiaolei Wu
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Guohua Zhong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Seth D Findley
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Perry Cregan
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Gary Stacey
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry; Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
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12
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Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'connor K, Prabhu AL, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:1063-78. [PMID: 17488239 DOI: 10.1111/j.1365-313x.2007.03112.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.
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Affiliation(s)
- Colin T Kelleher
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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13
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Wendl MC. Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping. BMC Bioinformatics 2007; 8:127. [PMID: 17442113 PMCID: PMC1868038 DOI: 10.1186/1471-2105-8-127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 04/18/2007] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Sulston score is a well-established, though approximate metric for probabilistically evaluating postulated clone overlaps in DNA fingerprint mapping. It is known to systematically over-predict match probabilities by various orders of magnitude, depending upon project-specific parameters. Although the exact probability distribution is also available for the comparison problem, it is rather difficult to compute and cannot be used directly in most cases. A methodology providing both improved accuracy and computational economy is required. RESULTS We propose a straightforward algebraic correction procedure, which takes the Sulston score as a provisional value and applies a power-law equation to obtain an improved result. Numerical comparisons indicate dramatically increased accuracy over the range of parameters typical of traditional agarose fingerprint mapping. Issues with extrapolating the method into parameter ranges characteristic of newer capillary electrophoresis-based projects are also discussed. CONCLUSION Although only marginally more expensive to compute than the raw Sulston score, the correction provides a vastly improved probabilistic description of hypothesized clone overlaps. This will clearly be important in overlap assessment and perhaps for other tasks as well, for example in using the ranking of overlap probabilities to assist in clone ordering.
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Affiliation(s)
- Michael C Wendl
- Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.
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14
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Osoegawa K, Vessere GM, Li Shu C, Hoskins RA, Abad JP, de Pablos B, Villasante A, de Jong PJ. BAC clones generated from sheared DNA. Genomics 2006; 89:291-9. [PMID: 17098394 PMCID: PMC1909752 DOI: 10.1016/j.ygeno.2006.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 09/15/2006] [Accepted: 10/06/2006] [Indexed: 01/31/2023]
Abstract
BAC libraries generated from restriction-digested genomic DNA display representational bias and lack some sequences. To facilitate completion of genome projects, procedures have been developed to create BACs from DNA physically sheared to create fragments extending up to 200 kb. The DNA fragments were repaired to create blunt ends and ligated to a new BAC vector. This approach has been tested by generating BAC libraries from Drosophila DNA with insert lengths between 50 and 150 kb. The libraries lack chimeric clone problems as determined by mapping paired BAC-end sequences to the assembled fly genome sequence. The utility of "sheared" libraries was demonstrated by closure of a previous clone gap and by isolation of clones from telomeric regions, which were notably absent from previous Drosophila BAC libraries.
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Affiliation(s)
- Kazutoyo Osoegawa
- Children's Hospital and Research Center at Oakland, 747 52nd Street, Oakland, CA 94609, USA.
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15
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Ng SHS, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJM, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 2006; 86:396-404. [PMID: 16026963 DOI: 10.1016/j.ygeno.2005.06.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 05/27/2005] [Accepted: 06/02/2005] [Indexed: 01/05/2023]
Abstract
A physical map of the Atlantic salmon (Salmo salar) genome was generated based on HindIII fingerprints of a publicly available BAC (bacterial artificial chromosome) library constructed from DNA isolated from a Norwegian male. Approximately 11.5 haploid genome equivalents (185,938 clones) were successfully fingerprinted. Contigs were first assembled via FPC using high-stringency (1e-16), and then end-to-end joins yielded 4354 contigs and 37,285 singletons. The accuracy of the contig assembly was verified by hybridization and PCR analysis using genetic markers. A subset of the BACs in the library contained few or no HindIII recognition sites in their insert DNA. BglI digestion fragment patterns of these BACs allowed us to identify three classes: (1) BACs containing histone genes, (2) BACs containing rDNA-repeating units, and (3) those that do not have BglI recognition sites. End-sequence analysis of selected BACs representing these three classes confirmed the identification of the first two classes and suggested that the third class contained highly repetitive DNA corresponding to tRNAs and related sequences.
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Affiliation(s)
- Siemon H S Ng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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16
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Wendl MC. Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a Priori Models. J Comput Biol 2005; 12:283-97. [PMID: 15857243 DOI: 10.1089/cmb.2005.12.283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We construct a combinatorially exact probability distribution for the problem of a priori clone overlap assessment in DNA fingerprint mapping. It is implemented as a general enumeration methodology using Bell's exponential polynomials. Established computational metrics do not consider the conditional nature of the problem. They dramatically overpredict actual match probabilities as a consequence. This elevates the rate of false-negative overlap declarations, which is consistent with previous validation studies. Increased measurement resolution does not significantly improve accuracy. We describe general trends in error behavior for intermediate-size DNA clones and discuss corresponding limits on the ability to assess certain overlaps.
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Affiliation(s)
- Michael C Wendl
- Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.
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17
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Khorasani MZ, Hennig S, Imre G, Asakawa S, Palczewski S, Berger A, Hori H, Naruse K, Mitani H, Shima A, Lehrach H, Wittbrodt J, Kondoh H, Shimizu N, Himmelbauer H. A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing. Mech Dev 2005; 121:903-13. [PMID: 15210195 DOI: 10.1016/j.mod.2004.03.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 03/29/2004] [Accepted: 03/30/2004] [Indexed: 01/11/2023]
Abstract
In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.
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Affiliation(s)
- Maryam Zadeh Khorasani
- Department of Vertebrate Genomics, Max-Planck-Institute of Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Dahlem, Germany
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18
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Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang SP, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, de Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC. A physical map of the chicken genome. Nature 2005; 432:761-4. [PMID: 15592415 DOI: 10.1038/nature03030] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 09/17/2004] [Indexed: 11/10/2022]
Abstract
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.
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Affiliation(s)
- John W Wallis
- Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
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19
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Meyers BC, Scalabrin S, Morgante M. Mapping and sequencing complex genomes: let's get physical! Nat Rev Genet 2004; 5:578-88. [PMID: 15266340 DOI: 10.1038/nrg1404] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
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20
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Moreira PN, Giraldo P, Cozar P, Pozueta J, Jiménez A, Montoliu L, Gutiérrez-Adán A. Efficient generation of transgenic mice with intact yeast artificial chromosomes by intracytoplasmic sperm injection. Biol Reprod 2004; 71:1943-7. [PMID: 15286029 DOI: 10.1095/biolreprod.104.032904] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The production of animals with large transgenes is an increasingly valuable tool in biotechnology and for genetic studies, including the characterization and manipulation of large genes and polygenic traits. In the present study, we describe an intracytoplasmic sperm injection (ICSI) method for the stable incorporation and phenotypic expression of large yeast artificial chromosomes (YAC) constructs of submegabase and megabase magnitude. By coinjecting spermatozoa and YACs into metaphase II oocytes, we were able to produce founders exhibiting germline transmission of an intact and functional transgene of 250 kilobases, carrying the mouse tyrosinase locus, used here as a reporter gene to rescue the albinism of recipient mice. More than 35% transgenesis was obtained for this YAC transgene. When compared with the pronuclear microinjection standard method, the efficiency of the ICSI-mediated YAC transfer system was significantly greater. In summary, we describe, for the first time, stable incorporation in the host genome and correct phenotypic expression of large DNA constructs mediated by ICSI.
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Affiliation(s)
- Pedro N Moreira
- Departamento de Reproducción Animal, INIA, 28040 Madrid, Spain
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21
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Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA. A set of BAC clones spanning the human genome. Nucleic Acids Res 2004; 32:3651-60. [PMID: 15247347 PMCID: PMC484185 DOI: 10.1093/nar/gkh700] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 06/22/2004] [Accepted: 06/22/2004] [Indexed: 11/15/2022] Open
Abstract
Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human fingerprint map, 99% of the current assembled sequence and has an effective resolving power of 79 kb. We have made the clone set publicly available, anticipating that it will generally facilitate FISH or array-CGH-based identification and characterization of chromosomal alterations relevant to disease.
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Affiliation(s)
- Martin Krzywinski
- BC Cancer Agency Genome Sciences Center and BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
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22
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Miyake T, Amemiya CT. BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C Toxicol Pharmacol 2004; 138:233-44. [PMID: 15533781 DOI: 10.1016/j.cca.2004.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Revised: 07/09/2004] [Accepted: 07/14/2004] [Indexed: 11/26/2022]
Abstract
The bacterial artificial chromosome (BAC) system is useful for creating a representation of the genomes of target species. The system is advantageous in that it can accommodate exogenous inserts that are very large (>100 kilobases, kb), thereby allowing entire eukaryotic genes (including flanking regulatory regions) to be encompassed in a single clone. The interest in BACs has recently been spawned by vast improvements in high throughput genomic sequencing such that comparisons of orthologous regions from different genomes (comparative genomics) are being routinely investigated, and comprise a significant component, of all major sequencing centers. In this review, we discuss the general principles of BAC cloning, the resources that are currently available, and some of the applications of the technology. It is not intended to be an exhaustive treatise; rather our goal is to provide a primer of the BAC technology in order to make readers aware of these resources and how they may utilize them in their own research programs.
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Affiliation(s)
- Tsutomu Miyake
- Molecular Genetics Department, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA.
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1512] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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Osoegawa K, Zhu B, Shu CL, Ren T, Cao Q, Vessere GM, Lutz MM, Jensen-Seaman MI, Zhao S, de Jong PJ. BAC resources for the rat genome project. Genome Res 2004; 14:780-5. [PMID: 15060022 PMCID: PMC383325 DOI: 10.1101/gr.2033904] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 12/28/2003] [Indexed: 02/07/2023]
Abstract
Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male Brown Norway (BN/SsNHsd) rat as a DNA source long before plans for rat genome sequencing had been launched. The second library was prepared from a highly inbred female (BN/SsNHsd/MCW) rat in support of the rat genome sequencing project. The use of an inbred rat strain is essential to avoid problems with genome assembly resulting from the difficulty of distinguishing haplotype variation from variation among duplicons. We have demonstrated the suitability of the library by using a detailed quality assessment of large insert sizes, narrow size distribution, consistent redundancy for many markers, and long-range continuity of BAC contig maps. The widespread use of the two libraries as an integral part of the rat genome project has led to the database annotations for many clones, providing rat researchers with a rich resource of BAC clones that can be screened in silico for genes of interest.
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Affiliation(s)
- Kazutoyo Osoegawa
- Children's Hospital and Research Center at Oakland, Oakland, California 94609, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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