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Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 2015; 25:445-58. [PMID: 25589440 PMCID: PMC4352887 DOI: 10.1101/gr.185579.114] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Drosophila melanogaster plays an important role in molecular,
genetic, and genomic studies of heredity, development, metabolism, behavior, and
human disease. The initial reference genome sequence reported more than a decade ago
had a profound impact on progress in Drosophila research, and
improving the accuracy and completeness of this sequence continues to be important to
further progress. We previously described improvement of the 117-Mb sequence in the
euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a
whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here,
we report an improved reference sequence of the single-copy and middle-repetitive
regions of the genome, produced using cytogenetic mapping to mitotic and polytene
chromosomes, clone-based finishing and BAC fingerprint verification, ordering of
scaffolds by alignment to cDNA sequences, incorporation of other map and sequence
data, and validation by whole-genome optical restriction mapping. These data
substantially improve the accuracy and completeness of the reference sequence and the
order and orientation of sequence scaffolds into chromosome arm assemblies.
Representation of the Y chromosome and other heterochromatic regions
is particularly improved. The new 143.9-Mb reference sequence, designated Release 6,
effectively exhausts clone-based technologies for mapping and sequencing. Highly
repeat-rich regions, including large satellite blocks and functional elements such as
the ribosomal RNA genes and the centromeres, are largely inaccessible to current
sequencing and assembly methods and remain poorly represented. Further significant
improvements will require sequencing technologies that do not depend on molecular
cloning and that produce very long reads.
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Affiliation(s)
- Roger A Hoskins
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
| | - Joseph W Carlson
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H Wan
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Soo Park
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ivonne Mendez
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel E Galle
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Benjamin W Booth
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Barret D Pfeiffer
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Reed A George
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Robert Svirskas
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Jacqueline Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Maria Carmela Accardo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Elisabetta Damia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - María Méndez-Lago
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Beatriz de Pablos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Olga V Demakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - A Bernardo Carvalho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, CEP 21944-970, Rio de Janeiro, Brazil
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Gerald M Rubin
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Gary H Karpen
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Susan E Celniker
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
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Salguero-Gómez R, Shefferson RP, Hutchings MJ. Plants do not count… or do they? New perspectives on the universality of senescence. THE JOURNAL OF ECOLOGY 2013; 101:545-554. [PMID: 23853389 PMCID: PMC3708120 DOI: 10.1111/1365-2745.12089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 03/01/2013] [Indexed: 05/23/2023]
Abstract
1. Senescence, the physiological decline that results in decreasing survival and/or reproduction with age, remains one of the most perplexing topics in biology. Most theories explaining the evolution of senescence (i.e. antagonistic pleiotropy, accumulation of mutations, disposable soma) were developed decades ago. Even though these theories have implicitly focused on unitary animals, they have also been used as the foundation from which the universality of senescence across the tree of life is assumed. 2. Surprisingly, little is known about the general patterns, causes and consequences of whole-individual senescence in the plant kingdom. There are important differences between plants and most animals, including modular architecture, the absence of early determination of cell lines between the soma and gametes, and cellular division that does not always shorten telomere length. These characteristics violate the basic assumptions of the classical theories of senescence and therefore call the generality of senescence theories into question. 3. This Special Feature contributes to the field of whole-individual plant senescence with five research articles addressing topics ranging from physiology to demographic modelling and comparative analyses. These articles critically examine the basic assumptions of senescence theories such as age-specific gene action, the evolution of senescence regardless of the organism's architecture and environmental filtering, and the role of abiotic agents on mortality trajectories. 4.Synthesis. Understanding the conditions under which senescence has evolved is of general importance across biology, ecology, evolution, conservation biology, medicine, gerontology, law and social sciences. The question 'why is senescence universal or why is it not?' naturally calls for an evolutionary perspective. Senescence is a puzzling phenomenon, and new insights will be gained by uniting methods, theories and observations from formal demography, animal demography and plant population ecology. Plants are more amenable than animals to experiments investigating senescence, and there is a wealth of published plant demographic data that enable interpretation of experimental results in the context of their full life cycles. It is time to make plants count in the field of senescence.
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Affiliation(s)
- Roberto Salguero-Gómez
- Evolutionary Biodemography Laboratory, Max Planck Institute for Demographic ResearchKonrad-Zuße straße 1, 18057, Rostock, Germany
- Centre for Biodiversity and Conservation Science, University of QueenslandGoddard Building #8, St Lucia, Qld, 4072, Australia
| | - Richard P Shefferson
- Odum School of Ecology, University of Georgia140 East Green Street, Athens, GA, 30601, USA
| | - Michael J Hutchings
- School of Life Sciences, University of SussexFalmer, Brighton, Sussex, BN1 9QG, UK
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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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Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.). G3-GENES GENOMES GENETICS 2012; 2:321-9. [PMID: 22413085 PMCID: PMC3291501 DOI: 10.1534/g3.111.001834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/21/2011] [Indexed: 11/21/2022]
Abstract
Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.
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Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AHJ, Janssen A, van Eijk MJT, Stormo K, Alberti A, Wincker P, Akhunov E, van der Vossen E, Feuillet C. Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome. BMC Genomics 2012; 13:47. [PMID: 22289472 PMCID: PMC3311077 DOI: 10.1186/1471-2164-13-47] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 01/30/2012] [Indexed: 01/28/2023] Open
Abstract
Background Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used recently to build the first physical map of a wheat chromosome and to complete the maize physical map. However, restriction fragments sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs and mis-assembled BACs in such large and repetitive genomes. Whole Genome Profiling (WGP™) was developed recently as a new sequence-based physical mapping technology and has the potential to limit this problem. Results A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology. We first adapted the WGP-based assembly methodology to cope with the complexity of the wheat genome. Then, the results showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and, more importantly with 3.5 times less mis-assembled BACs. Finally, we evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves assemblies performed with unpaired reads and with paired-end reads at low coverage, it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads. Conclusions Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP tags can support the efficient sequencing of BAC pools by enabling reliable assignment of sequence scaffolds to their BAC of origin, a feature that is of great interest when using BAC pooling strategies to reduce the cost of sequencing large genomes.
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Affiliation(s)
- Romain Philippe
- INRA-UBP, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brezet, 63100 Clermont- Ferrand, France
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6
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de Boer JM, Borm TJA, Jesse T, Brugmans B, Wiggers-Perebolte L, de Leeuw L, Tang X, Bryan GJ, Bakker J, van Eck HJ, Visser RGF. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome. BMC Genomics 2011; 12:594. [PMID: 22142254 PMCID: PMC3261212 DOI: 10.1186/1471-2164-12-594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). RESULTS First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. CONCLUSIONS The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalstesteeg 1, 6708 PD Wageningen, The Netherlands.
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7
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Ragupathy R, Rathinavelu R, Cloutier S. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 2011; 12:217. [PMID: 21554714 PMCID: PMC3113786 DOI: 10.1186/1471-2164-12-217] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/09/2011] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. RESULTS The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. CONCLUSION The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.
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Affiliation(s)
- Raja Ragupathy
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
| | - Rajkumar Rathinavelu
- Genomics & Bioinformatics Division, ITC Research & Development Centre, Bangalore, India
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada
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Frenkel Z, Paux E, Mester D, Feuillet C, Korol A. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. BMC Bioinformatics 2010; 11:584. [PMID: 21118513 PMCID: PMC3098104 DOI: 10.1186/1471-2105-11-584] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/30/2010] [Indexed: 11/25/2022] Open
Abstract
Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs). Results To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.
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Affiliation(s)
- Zeev Frenkel
- University of Haifa, Institute of Evolution, Haifa 31905, Israel.
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A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). PLoS One 2010; 5:e11974. [PMID: 20700486 PMCID: PMC2916840 DOI: 10.1371/journal.pone.0011974] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Background The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences. Methodology/Principal Findings A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly. Conclusions/Significance The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.
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Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics 2010; 11:204. [PMID: 20346114 PMCID: PMC2865496 DOI: 10.1186/1471-2164-11-204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 03/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. RESULTS We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. CONCLUSIONS We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.
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Affiliation(s)
- Simone Scalabrin
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli, Via J Linussio 51, 33100 Udine, Italy
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Mun JH, Kwon SJ, Yang TJ, Kim HS, Choi BS, Baek S, Kim JS, Jin M, Kim JA, Lim MH, Lee SI, Kim HI, Kim H, Lim YP, Park BS. The first generation of a BAC-based physical map of Brassica rapa. BMC Genomics 2008; 9:280. [PMID: 18549474 PMCID: PMC2432078 DOI: 10.1186/1471-2164-9-280] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 06/12/2008] [Indexed: 11/30/2022] Open
Abstract
Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.
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Affiliation(s)
- Jeong-Hwan Mun
- Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, 225 Seodun-dong, Gwonseon-gu, Suwon 441-707, South Korea.
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12
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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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13
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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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14
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A BAC library of Beta vulgaris L. for the targeted isolation of centromeric DNA and molecular cytogenetics of Beta species. Genetica 2008; 135:157-67. [DOI: 10.1007/s10709-008-9265-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
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15
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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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16
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Xu Z, Kohel RJ, Song G, Cho J, Yu J, Yu S, Tomkins J, Yu JZ. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics 2008; 9:108. [PMID: 18307816 PMCID: PMC2270834 DOI: 10.1186/1471-2164-9-108] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 02/28/2008] [Indexed: 11/29/2022] Open
Abstract
Background Upland cotton (G. hirsutum L.) is the leading fiber crop worldwide. Genetic improvement of fiber quality and yield is facilitated by a variety of genomics tools. An integrated genetic and physical map is needed to better characterize quantitative trait loci and to allow for the positional cloning of valuable genes. However, developing integrated genomic tools for complex allotetraploid genomes, like that of cotton, is highly experimental. In this report, we describe an effective approach for developing an integrated physical framework that allows for the distinguishing between subgenomes in cotton. Results A physical map has been developed with 220 and 115 BAC contigs for homeologous chromosomes 12 and 26, respectively, covering 73.49 Mb and 34.23 Mb in physical length. Approximately one half of the 220 contigs were anchored to the At subgenome only, while 48 of the 115 contigs were allocated to the Dt subgenome only. Between the two chromosomes, 67 contigs were shared with an estimated overall physical similarity between the two chromosomal homeologs at 40.0 %. A total of 401 fiber unigenes plus 214 non-fiber unigenes were located to chromosome 12 while 207 fiber unigenes plus 183 non-fiber unigenes were allocated to chromosome 26. Anchoring was done through an overgo hybridization approach and all anchored ESTs were functionally annotated via blast analysis. Conclusion This integrated genomic map describes the first pair of homoeologous chromosomes of an allotetraploid genome in which BAC contigs were identified and partially separated through the use of chromosome-specific probes and locus-specific genetic markers. The approach used in this study should prove useful in the construction of genome-wide physical maps for polyploid plant genomes including Upland cotton. The identification of Gene-rich islands in the integrated map provides a platform for positional cloning of important genes and the targeted sequencing of specific genomic regions.
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Affiliation(s)
- Zhanyou Xu
- USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, 2881 F&B Road, College Station, TX 77845, USA.
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17
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Bakkeren G, Jiang G, Warren RL, Butterfield Y, Shin H, Chiu R, Linning R, Schein J, Lee N, Hu G, Kupfer DM, Tang Y, Roe BA, Jones S, Marra M, Kronstad JW. Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals. Fungal Genet Biol 2006; 43:655-66. [PMID: 16793293 DOI: 10.1016/j.fgb.2006.04.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Revised: 04/06/2006] [Accepted: 04/07/2006] [Indexed: 11/25/2022]
Abstract
Sex in basidiomycete fungi is controlled by tetrapolar mating systems in which two unlinked gene complexes determine up to thousands of mating specificities, or by bipolar systems in which a single locus (MAT) specifies different sexes. The genus Ustilago contains bipolar (Ustilago hordei) and tetrapolar (Ustilago maydis) species and sexual development is associated with infection of cereal hosts. The U. hordei MAT-1 locus is unusually large (approximately 500 kb) and recombination is suppressed in this region. We mapped the genome of U. hordei and sequenced the MAT-1 region to allow a comparison with mating-type regions in U. maydis. Additionally the rDNA cluster in the U. hordei genome was identified and characterized. At MAT-1, we found 47 genes along with a striking accumulation of retrotransposons and repetitive DNA; the latter features were notably absent from the corresponding U. maydis regions. The tetrapolar mating system may be ancestral and differences in pathogenic life style and potential for inbreeding may have contributed to genome evolution.
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Affiliation(s)
- Guus Bakkeren
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, Summerland, BC.
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18
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Shultz JL, Yesudas C, Yaegashi S, Afzal AJ, Kazi S, Lightfoot DA. Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest'): tools for structural and functional genomics. PLANT METHODS 2006; 2:9. [PMID: 16725032 PMCID: PMC1524761 DOI: 10.1186/1746-4811-2-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 05/25/2006] [Indexed: 05/04/2023]
Abstract
BACKGROUND The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4. RESULTS The first MTP, named MTP2, was 14,208 clones (of mean insert size 140 kbp) picked from the 5,597 contigs of build 2. MTP2 was constructed from three BAC libraries (BamHI (B), HindIII (H) and EcoRI (E) inserts). MTP2 encompassed the contigs of build 3 that derived from build 2 by a series of contig merges. MTP2 encompassed 2 Gbp compared to the soybean haploid genome of 1 Gbp and does not distinguish regions by ploidy. The second and third MTPs, called MTP4BH and MTP4E, were each based on build 4. Each was semi-automatically selected from 2,854 contigs. MTP4BH was 4,608 B and H insert clones of mean size 173 kbp in the large (27.6 kbp) T-DNA vector pCLD04541. MTP4BH was suitable for plant transformation and functional genomics. MTP4E was 4,608 BAC clones with large inserts (mean 175 kbp) in the small (7.5 kbp) pECBAC1 vector. MTP4E was suitable for DNA sequencing. MTP4BH and MTP4E clones each encompassed about 0.8 Gbp, the 0.7 Gbp diploid regions and 0.05 Gbp each from the tetraploid and octoploid regions. MTP2 and MTP4BH were used for BAC-end sequencing, EST integration, micro-satellite integration into the physical map and high information content fingerprinting. MTP4E will be used for genome sequence by pooled genomic clone index. CONCLUSION Each MTP and associated BES will be useful to deconvolute and ultimately finish the whole genome shotgun sequence of soybean.
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Affiliation(s)
- JL Shultz
- Dept of Soybean Genetics, United States Department of Agriculture, Stoneville, MS 38776, USA
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | - C Yesudas
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | - S Yaegashi
- Dept of Soybean Genetics, United States Department of Agriculture, Stoneville, MS 38776, USA
- Dept of Bioinformatics, University of Tokyo, Tokyo, Japan
| | - AJ Afzal
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | | | - DA Lightfoot
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
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Cheng CH, Chung MC, Liu SM, Chen SK, Kao FY, Lin SJ, Hsiao SH, Tseng IC, Hsing YIC, Wu HP, Chen CS, Shaw JF, Wu J, Matsumoto T, Sasaki T, Chen HH, Chow TY. A fine physical map of the rice chromosome 5. Mol Genet Genomics 2005; 274:337-45. [PMID: 16261349 DOI: 10.1007/s00438-005-0039-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.
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Nelson WM, Bharti AK, Butler E, Wei F, Fuks G, Kim H, Wing RA, Messing J, Soderlund C. Whole-genome validation of high-information-content fingerprinting. PLANT PHYSIOLOGY 2005; 139:27-38. [PMID: 16166258 PMCID: PMC1203355 DOI: 10.1104/pp.105.061978] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.
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Affiliation(s)
- William M Nelson
- Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, 85721, USA
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Atibalentja N, Bekal S, Domier LL, Niblack TL, Noel GR, Lambert KN. A genetic linkage map of the soybean cyst nematode Heterodera glycines. Mol Genet Genomics 2005; 273:273-81. [PMID: 15902493 DOI: 10.1007/s00438-005-1125-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Accepted: 01/25/2005] [Indexed: 11/24/2022]
Abstract
A genetic linkage map of the soybean cyst nematode (SCN) Heterodera glycines was constructed using a population of F2 individuals obtained from matings between two highly inbred SCN lines, TN16 and TN20. The AFLP fingerprinting technique was used to genotype 63 F2 progeny with two restriction enzyme combinations (EcoRI/MseI and PstI/TaqI) and 38 primer combinations. The same F2 population was also genotyped for Hg-cm-1 (H. glycines chorismate mutase-1), a putative virulence gene, using real-time quantitative PCR. Some of the markers were found to be distributed non-randomly. Even so, of the 230 markers analyzed, 131 could be mapped onto ten linkage groups at a minimum LOD of 3.0, for a total map distance of 539 cM. The Hg-cm-1 locus mapped to linkage group III together with 16 other markers. The size of the H. glycines genome was estimated to be in the range of 630-743 cM, indicating that the current map represents 73-86% of the genome, with a marker density of one per 4.5 cM, and a physical/genetic distance ratio of between 124 kb/cM and 147 kb/cM. This genetic map will be of great assistance in mapping H. glycines markers to genes of interest, such as nematode virulence genes and genes that control aspects of nematode parasitism.
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Affiliation(s)
- N Atibalentja
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, USA
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Xu Z, Sun S, Covaleda L, Ding K, Zhang A, Wu C, Scheuring C, Zhang HB. Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality. Genomics 2005; 84:941-51. [PMID: 15533711 DOI: 10.1016/j.ygeno.2004.08.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Accepted: 08/18/2004] [Indexed: 11/19/2022]
Abstract
Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.
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Affiliation(s)
- Zhanyou Xu
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M University, College Station, TX 77843-2123, USA
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23
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Xu Z, van den Berg MA, Scheuring C, Covaleda L, Lu H, Santos FA, Uhm T, Lee MK, Wu C, Liu S, Zhang HB. Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum. Nucleic Acids Res 2005; 33:e50. [PMID: 15767275 PMCID: PMC1065262 DOI: 10.1093/nar/gni037] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.
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Affiliation(s)
| | | | | | | | - Hong Lu
- Department of Computer Science, Texas A&M UniversityCollege Station, TX 77843, USA
| | | | | | | | | | - Steve Liu
- Department of Computer Science, Texas A&M UniversityCollege Station, TX 77843, USA
| | - Hong-Bin Zhang
- To whom correspondence should be addressed. Tel: +1 979 862 2244; Fax: +1 979 862 4790;
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Luo S, Hall AE, Hall SE, Preuss D. Whole-genome fractionation rapidly purifies DNA from centromeric regions. Nat Methods 2004; 1:67-71. [PMID: 15782155 DOI: 10.1038/nmeth703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Accepted: 08/03/2004] [Indexed: 11/09/2022]
Abstract
The condensed centromeric regions of higher eukaryotic chromosomes contain satellite sequences, transposons and retroelements, as well as transcribed genes that perform a variety of functions. These chromosomal domains nucleate kinetochores, mediate sister chromatid cohesion and inhibit recombination, yet their characterization has often lagged behind that of chromosome arms. Here, we describe a whole-genome fractionation technique that rapidly identifies bacterial artificial chromosome (BAC) clones derived from plant centromeric regions. This approach, which relies on hybridization of methylated genomic DNA, revealed BACs that correspond to the genetically mapped and sequenced Arabidopsis thaliana centromeric regions. Extending this method to other species in the Brassicaceae family identified centromere-linked clones and provided genome-wide estimates of methylated DNA abundance. Sequencing these clones will elucidate the changes that occur during plant centromere evolution. This genomic fractionation technique could identify centromeric DNA in genomes with similar methylation and repetitive DNA content, including those from crops and mammals.
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Affiliation(s)
- Song Luo
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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25
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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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26
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Hong CP, Lee SJ, Park JY, Plaha P, Park YS, Lee YK, Choi JE, Kim KY, Lee JH, Lee J, Jin H, Choi SR, Lim YP. Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences. Mol Genet Genomics 2004; 271:709-16. [PMID: 15197578 DOI: 10.1007/s00438-004-1021-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 04/30/2004] [Indexed: 10/26/2022]
Abstract
We estimated the genome size of Korean ginseng (Panax ginseng C.A. Meyer), a medicinal herb, constructed a HindIII BAC library, and analyzed BAC-end sequences to provide an initial characterization of the library. The 1C nuclear DNA content of Korean ginseng was estimated to be 3.33 pg (3.12 x 10(3) Mb). The BAC library consists of 106,368 clones with an average size of 98.61 kb, amounting to 3.34 genome equivalents. Sequencing of 2167 BAC clones generated 2492 BAC-end sequences with an average length of 400 bp. Analysis using BLAST and motif searches revealed that 10.2%, 20.9% and 3.8% of the BAC-end sequences contained protein-coding regions, transposable elements and microsatellites, respectively. A comparison of the functional categories represented by the protein-coding regions found in BAC-end sequences with those of Arabidopsis revealed that proteins pertaining to energy metabolism, subcellular localization, cofactor requirement and transport facilitation were more highly represented in the P. ginseng sample. In addition, a sequence encoding a glucosyltransferase-like protein implicated in the ginsenoside biosynthesis pathway was also found. The majority of the transposable element sequences found belonged to the gypsy type (67.6%), followed by copia (11.7%) and LINE (8.0%) retrotransposons, whereas DNA transposons accounted for only 2.1% of the total in our sequence sample. Higher levels of transposable elements than protein-coding regions suggest that mobile elements have played an important role in the evolution of the genome of Korean ginseng, and contributed significantly to its complexity. We also identified 103 microsatellites with 3-38 repeats in their motifs. The BAC library and BAC-end sequences will serve as a useful resource for physical mapping, positional cloning and genome sequencing of P. ginseng.
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Affiliation(s)
- C P Hong
- Department of Horticulture, and Genome Research Center, Chungnam National University, 305-764, Daejeon, Korea
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27
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Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hübner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res 2004; 14:766-79. [PMID: 15060021 PMCID: PMC383324 DOI: 10.1101/gr.2336604] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Accepted: 02/16/2004] [Indexed: 01/08/2023]
Abstract
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.
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Affiliation(s)
- Martin Krzywinski
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6
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28
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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: 1524] [Impact Index Per Article: 76.2] [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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29
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Aerts J, Crooijmans R, Cornelissen S, Hemmatian K, Veenendaal T, Jaadar A, van der Poel J, Fillon V, Vignal A, Groenen M. Integration of chicken genomic resources to enable whole-genome sequencing. Cytogenet Genome Res 2004; 102:297-303. [PMID: 14970720 DOI: 10.1159/000075766] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 07/30/2003] [Indexed: 11/19/2022] Open
Abstract
Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome walking experiments. Second, HINdIII digestion fingerprints were created for all BACs of the Wageningen chicken BAC library. Third, cytogenetic positions of BACs were assigned by FISH. These integrated resources will facilitate further chromosome-walking experiments and whole-genome sequencing.
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Affiliation(s)
- J Aerts
- Animal Breeding and Genetics Group, Wageningen University, Wageningen, The Netherlands.
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30
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Wu C, Sun S, Nimmakayala P, Santos FA, Meksem K, Springman R, Ding K, Lightfoot DA, Zhang HB. A BAC- and BIBAC-based physical map of the soybean genome. Genome Res 2004; 14:319-26. [PMID: 14718376 PMCID: PMC327108 DOI: 10.1101/gr.1405004] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2003] [Accepted: 11/18/2003] [Indexed: 11/24/2022]
Abstract
Genome-wide physical maps are crucial to many aspects of advanced genome research. We report a genome-wide, bacterial artificial chromosome (BAC) and plant-transformation-competent binary large-insert plasmid clone (hereafter BIBAC)-based physical map of the soybean genome. The map was constructed from 78001 clones from five soybean BAC and BIBAC libraries representing 9.6 haploid genomes and three cultivars, and consisted of 2905 BAC/BIBAC contigs, estimated to span 1408 Mb in physical length. We evaluated the reliability of the map contigs using different contig assembly strategies, independent contig building methods, DNA marker hybridization, and different fingerprinting methods, and the results showed that the contigs were assembled properly. Furthermore, we tested the feasibility of integrating the physical map with the existing soybean composite genetic map using 388 DNA markers. The results further confirmed the nature of the ancient tetraploid origin of soybean and indicated that it is feasible to integrate the physical map with the linkage map even though greater efforts are needed. This map represents the first genome-wide, BAC/BIBAC-based physical map of the soybean genome and would provide a platform for advanced genome research of soybean and other legume species. The inclusion of BIBACs in the map would streamline the utility of the map for positional cloning of genes and QTLs, and functional analysis of soybean genomic sequences.
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Affiliation(s)
- Chengcang Wu
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, Texas A&MUniversity, College Station, Texas 77843-2123, USA
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31
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Engler FW, Hatfield J, Nelson W, Soderlund CA. Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res 2003; 13:2152-63. [PMID: 12915486 PMCID: PMC403717 DOI: 10.1101/gr.1068603] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This study discusses three software tools, the first two aid in integrating sequence with an FPC physical map and the third automatically selects a minimal tiling path given genomic draft sequence and BAC end sequences. The first tool, FSD (FPC Simulated Digest), takes a sequenced clone and adds it back to the map based on a fingerprint generated by an in silico digest of the clone. This allows verification of sequenced clone positions and the integration of sequenced clones that were not originally part of the FPC map. The second tool, BSS (Blast Some Sequence), takes a query sequence and positions it on the map based on sequence associated with the clones in the map. BSS has multiple uses as follows: (1) When the query is a file of marker sequences, they can be added as electronic markers. (2) When the query is draft sequence, the results of BSS can be used to close gaps in a sequenced clone or the physical map. (3) When the query is a sequenced clone and the target is BAC end sequences, one may select the next clone for sequencing using both sequence comparison results and map location. (4) When the query is whole-genome draft sequence and the target is BAC end sequences, the results can be used to select many clones for a minimal tiling path at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole-genome shotgun from Syngenta.
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Affiliation(s)
- Friedrich W Engler
- Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721, USA
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32
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Srinivasan J, Sinz W, Jesse T, Wiggers-Perebolte L, Jansen K, Buntjer J, van der Meulen M, Sommer RJ. An integrated physical and genetic map of the nematode Pristionchus pacificus. Mol Genet Genomics 2003; 269:715-22. [PMID: 12884007 DOI: 10.1007/s00438-003-0881-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 06/06/2003] [Indexed: 11/26/2022]
Abstract
The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.
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Affiliation(s)
- J Srinivasan
- Abteilung für Evolutionsbiologie, Max-Planck Institut für Entwicklungsbiologie, Spemannstrasse 37, 72076 Tübingen, Germany
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33
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Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps. Genome Res 2003; 13:1244-9. [PMID: 12799356 PMCID: PMC403654 DOI: 10.1101/gr.819303] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for several genomes, including those of human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria, poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can also load into the software lists of particular clones of interest and view their fingerprints. iCE is being used at our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae, and several fungal genome bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine.
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Affiliation(s)
- Christopher D Fjell
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada
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34
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Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res 2003; 13:940-53. [PMID: 12727910 PMCID: PMC430903 DOI: 10.1101/gr.904303] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2002] [Accepted: 02/26/2003] [Indexed: 11/24/2022]
Abstract
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.
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Affiliation(s)
- Daniel R Fuhrmann
- Department of Electrical Engineering, Washington University, St. Louis, Missouri 63130, USA
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35
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Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2002; 133:609-46. [PMID: 12470823 DOI: 10.1016/s1096-4959(02)00167-7] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.
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Affiliation(s)
- Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA.
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36
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Schein JE, Tangen KL, Chiu R, Shin H, Lengeler KB, MacDonald WK, Bosdet I, Heitman J, Jones SJM, Marra MA, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res 2002; 12:1445-53. [PMID: 12213782 PMCID: PMC186652 DOI: 10.1101/gr.81002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2002] [Accepted: 07/03/2002] [Indexed: 11/25/2022]
Abstract
The basidiomycete fungus Cryptococcus neoformans is an important opportunistic pathogen of humans that poses a significant threat to immunocompromised individuals. Isolates of C. neoformans are classified into serotypes (A, B, C, D, and AD) based on antigenic differences in the polysaccharide capsule that surrounds the fungal cells. Genomic and EST sequencing projects are underway for the serotype D strain JEC21 and the serotype A strain H99. As part of a genomics program for C. neoformans, we have constructed fingerprinted bacterial artificial chromosome (BAC) clone physical maps for strains H99 and JEC21 to support the genomic sequencing efforts and to provide an initial comparison of the two genomes. The BAC clones represented an estimated 10-fold redundant coverage of the genomes of each serotype and allowed the assembly of 20 contigs each for H99 and JEC21. We found that the genomes of the two strains are sufficiently distinct to prevent coassembly of the two maps when combined fingerprint data are used to construct contigs. Hybridization experiments placed 82 markers on the JEC21 map and 102 markers on the H99 map, enabling contigs to be linked with specific chromosomes identified by electrophoretic karyotyping. These markers revealed both extensive similarity in gene order (conservation of synteny) between JEC21 and H99 as well as examples of chromosomal rearrangements including inversions and translocations. Sequencing reads were generated from the ends of the BAC clones to allow correlation of genomic shotgun sequence data with physical map contigs. The BAC maps therefore represent a valuable resource for the generation, assembly, and finishing of the genomic sequence of both JEC21 and H99. The physical maps also serve as a link between map-based and sequence-based data, providing a powerful resource for continued genomic studies
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Affiliation(s)
- Jacqueline E Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
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37
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Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang LS, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B. A fine physical map of the rice chromosome 4. Genome Res 2002; 12:817-23. [PMID: 11997348 PMCID: PMC186569 DOI: 10.1101/gr.48902] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies.
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Affiliation(s)
- Qiang Zhao
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yu Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Zhukuan Cheng
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Mingsheng Chen
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Shengyue Wang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Qi Feng
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yucheng Huang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Ying Li
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yesheng Tang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Bo Zhou
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Zhehua Chen
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Shuliang Yu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Jingjie Zhu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Xin Hu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Jie Mu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Kai Ying
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Pei Hao
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Lei Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yiqi Lu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Lei S. Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yilei Liu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Zhen Yu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Danlin Fan
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Qijun Weng
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Ling Chen
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Tingting Lu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Xiaohui Liu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Peixin Jia
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Tongguo Sun
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yongrui Wu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yujun Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Ying Lu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Can Li
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Rong Wang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Haiyan Lei
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Tao Li
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Hao Hu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Mei Wu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Runquan Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Jianping Guan
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Jia Zhu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Gang Fu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Minghong Gu
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Guofan Hong
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Yongbiao Xue
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Rod Wing
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Jiming Jiang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; Chinese Human Genome Center at Shanghai, Shanghai 201203, China; Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China
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Mayer K, Mewes HW. How can we deliver the large plant genomes? Strategies and perspectives. CURRENT OPINION IN PLANT BIOLOGY 2002; 5:173-177. [PMID: 11856615 DOI: 10.1016/s1369-5266(02)00235-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The first sequenced plant genome, from the small mustard plant Arabidopsis thaliana, was published at the end of 2000. The sequencing of the rice genome is well under way. The sizes of plant genomes vary by a factor of up to 1000, and many important crop plants have genomes that are several times larger than the human genome. To gain insight into the gene toolbox of plant species, numerous large-scale EST sequencing projects have been launched successfully, and analysis procedures are constantly being refined to add maximum value to the sequence data. In addition, an alternative approach to exclude repetitive noncoding DNA and to enrich sequence libraries for gene-containing genomic regions has been developed. This strategy has the potential to deliver information about both genes and regulatory regions outside the transcribed regions.
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Affiliation(s)
- Klaus Mayer
- Munich Information Centre for Protein Sequences (MIPS), Institute for Bioinformatics, GSF-National Research Centre for Environment and Health, Ingolstädter Landstrasse 1, 85758 Neuherberg, Germany.
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Makrigiannis AP, Pau AT, Schwartzberg PL, McVicar DW, Beck TW, Anderson SK. A BAC contig map of the Ly49 gene cluster in 129 mice reveals extensive differences in gene content relative to C57BL/6 mice. Genomics 2002; 79:437-44. [PMID: 11863373 DOI: 10.1006/geno.2002.6724] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The murine Ly49 gene family is functionally analogous to the human killer cell Ig-like receptor (KIR) family of class I major histocompatibility complex (MHC) receptors. The number of KIR genes varies dramatically between individuals; however, the organization of the Ly49 genes has only been determined for the C57BL/6 (B6) mouse. The organization of the 129 Ly49 loci was determined from a BAC contig map by PCR and Southern blot analysis. In addition to the 10 Ly49 genes known from previous studies of the 129/J strain, 8 new genes were localized to the 129 Ly49 cluster. A gene order of Ly49q(1), e, (v, q(2)), e/c(2), l/r, s, t, e/c(1), r, u, u/i, i(1), g, p/d, (i(2), p), and o was determined. The 129 Ly49 gene cluster is predicted to span approximately 600 kb. These results indicate that Ly49 gene numbers can be significantly different between inbred mouse strains, analogous to the haplotype differences observed in the human KIR genes.
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Affiliation(s)
- Andrew P Makrigiannis
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland 21702-1201, USA
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40
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Chang YL, Tao Q, Scheuring C, Ding K, Meksem K, Zhang HB. An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 2001; 159:1231-42. [PMID: 11729165 PMCID: PMC1461882 DOI: 10.1093/genetics/159.3.1231] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genome of the model plant species Arabidopsis thaliana has recently been sequenced. To accelerate its current genome research, we developed a whole-genome, BAC/BIBAC-based, integrated physical, genetic, and sequence map of the A. thaliana ecotype Columbia. This new map was constructed from the clones of a new plant-transformation-competent BIBAC library and is integrated with the existing sequence map. The clones were restriction fingerprinted by DNA sequencing gel-based electrophoresis, assembled into contigs, and anchored to an existing genetic map. The map consists of 194 BAC/BIBAC contigs, spanning 126 Mb of the 130-Mb Arabidopsis genome. A total of 120 contigs, spanning 114 Mb, were anchored to the chromosomes of Arabidopsis. Accuracy of the integrated map was verified using the existing physical and sequence maps and numerous DNA markers. Integration of the new map with the sequence map has enabled gap closure of the sequence map and will facilitate functional analysis of the genome sequence. The method used here has been demonstrated to be sufficient for whole-genome physical mapping from large-insert random bacterial clones and thus is applicable to rapid development of whole-genome physical maps for other species.
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Affiliation(s)
- Y L Chang
- Department of Soil and Crop Sciences and Crop Biotechnology Center, Texas A&M University, College Station, Texas 77843-2123, USA
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41
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Gindullis F, Dechyeva D, Schmidt T. Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis. Genome 2001. [DOI: 10.1139/g01-076] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have constructed a sugar beet bacterial artificial chromosome (BAC) library of the chromosome mutant PRO1. This Beta vulgaris mutant carries a single chromosome fragment of 6-9 Mbp that is derived from the wild beet Beta procumbens and is transmitted efficiently in meiosis and mitosis. The library consists of 50 304 clones, with an average insert size of 125 kb. Filter hybridizations revealed that approximately 3.1% of the clones contain mitochondrial or chloroplast DNA. Based on a haploid genome size of 758 Mbp, the library represents eight genome equivalents. Thus, there is a greater than 99.96% probability that any sequence of the PRO1 genome can be found in the library. Approximately 0.2% of the clones hybridized with centromeric sequences of the PRO1 minichromosome. Using the identified BAC clones in fluorescence in situ hybridization experiments with PRO1 and B. procumbens chromosome spreads, their wild-beet origin and centromeric localization were demonstrated. Comparative Southern hybridization of pulsed-field separated PRO1 DNA and BAC inserts indicate that the centromeric region of the minichromosome is represented by overlapping clones in the library. Therefore, the PRO1 BAC library provides a useful tool for the characterization of a single plant centromere and is a valuable resource for sugar beet genome analysis.Key words: Beta vulgaris, BAC library, Beta procumbens minichromosome, centromere, FISH.
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42
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Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB. Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 2001; 158:1711-24. [PMID: 11514457 PMCID: PMC1461754 DOI: 10.1093/genetics/158.4.1711] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome-wide physical mapping with bacteria-based large-insert clones (e.g., BACs, PACs, and PBCs) promises to revolutionize genomics of large, complex genomes. To accelerate rice and other grass species genome research, we developed a genome-wide BAC-based map of the rice genome. The map consists of 298 BAC contigs and covers 419 Mb of the 430-Mb rice genome. Subsequent analysis indicated that the contigs constituting the map are accurate and reliable. Particularly important to proficiency were (1) a high-resolution, high-throughput DNA sequencing gel-based electrophoretic method for BAC fingerprinting, (2) the use of several complementary large-insert BAC libraries, and (3) computer-aided contig assembly. It has been demonstrated that the fingerprinting method is not significantly influenced by repeated sequences, genome size, and genome complexity. Use of several complementary libraries developed with different restriction enzymes minimized the "gaps" in the physical map. In contrast to previous estimates, a clonal coverage of 6.0-8.0 genome equivalents seems to be sufficient for development of a genome-wide physical map of approximately 95% genome coverage. This study indicates that genome-wide BAC-based physical maps can be developed quickly and economically for a variety of plant and animal species by restriction fingerprint analysis via DNA sequencing gel-based electrophoresis.
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Affiliation(s)
- Q Tao
- Department of Soil and Crop Sciences and Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123, USA
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43
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Haupt W, Fischer TC, Winderl S, Fransz P, Torres-Ruiz RA. The centromere1 (CEN1) region of Arabidopsis thaliana: architecture and functional impact of chromatin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2001; 27:285-296. [PMID: 11532174 DOI: 10.1046/j.1365-313x.2001.01087.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have analysed the centromere 1 (CEN1) of Arabidopsis thaliana by integration of genetic, sequence and fluorescence in situ hybridisation (FISH) data. CEN1 is considered to include the centromeric core and the flanking left and right pericentromeric regions, which are distinct parts by structural and/or functional properties. CEN1 pericentromeres are composed of different dispersed repetitive elements, sometimes interrupted by functional genes. In contrast the CEN1 core is more uniformly structured harbouring only two different repeats. The presented analysis reveals aspects concerning distribution and effects of the uniformly shaped heterochromatin, which covers all CEN1 regions. A lethal mutation tightly linked to CEN1 enabled us to measure recombination frequencies within the heterochromatin in detail. In the left pericentromere, the change from eu- to heterochromatin is accompanied by a gradual change in sequence composition but by an extreme change in recombination frequency (from normal to 53-fold decrease) which takes place within a small region spanning 15 kb. Generally, heterochromatin is known to suppress recombination. However, the same analysis reveals that left and right pericentromere, though similar in sequence composition, differ markedly in suppression (53-fold versus 10-fold). The centromeric core exhibits at least 200-fold if not complete suppression. We discuss whether differences in (fine) composition reflect quantitative and qualitative differences in binding sites for heterochromatin proteins and in turn render different functional properties. Based on the presented data we estimate the sizes of Arabidopsis centromeres. These are typical for regional centromeres of higher eukaryotes and range from 4.4 Mb (CEN1) to 3.55 Mb (CEN4).
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Affiliation(s)
- W Haupt
- Lehrstuhl für Genetik, Technische Universität München, Germany
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44
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Abstract
Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.
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Affiliation(s)
- E D Green
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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45
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Affiliation(s)
- R Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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46
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Abstract
The completion of the Arabidopsis thaliana (mustard weed) genome sequence constitutes a major breakthrough in plant biology. It will revolutionize how we answer questions about the biology and evolution of plants as well as how we confront and resolve world-wide agricultural problems.
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Affiliation(s)
- A Theologis
- Plant Gene Expression Center, Buchanan Street, Albany, CA 94710, USA.
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47
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Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 2001; 11:483-96. [PMID: 11230172 PMCID: PMC311044 DOI: 10.1101/gr.169601] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2000] [Accepted: 01/09/2001] [Indexed: 01/20/2023]
Abstract
A 30-fold redundant human bacterial artificial chromosome (BAC) library with a large average insert size (178 kb) has been constructed to provide the intermediate substrate for the international genome sequencing effort. The DNA was obtained from a single anonymous volunteer, whose identity was protected through a double-blind donor selection protocol. DNA fragments were generated by partial digestion with EcoRI (library segments 1--4: 24-fold) and MboI (segment 5: sixfold) and cloned into the pBACe3.6 and pTARBAC1 vectors, respectively. The quality of the library was assessed by extensive analysis of 169 clones for rearrangements and artifacts. Eighteen BACs (11%) revealed minor insert rearrangements, and none was chimeric. This BAC library, designated as "RPCI-11," has been used widely as the central resource for insert-end sequencing, clone fingerprinting, high-throughput sequence analysis and as a source of mapped clones for diagnostic and functional studies.
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Affiliation(s)
- K Osoegawa
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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48
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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. [PMID: 11237011 DOI: 10.1038/35057062] [Citation(s) in RCA: 14641] [Impact Index Per Article: 636.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Affiliation(s)
- E S Lander
- Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, MA 02142, USA.
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49
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McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H. A physical map of the human genome. Nature 2001; 409:934-41. [PMID: 11237014 DOI: 10.1038/35057157] [Citation(s) in RCA: 549] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.
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Affiliation(s)
- J D McPherson
- Washington University School of Medicine, Genome Sequencing Center, Department of Genetics, St. Louis, Missouri 63108, USA.
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50
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Beck TW, Menninger J, Voigt G, Newmann K, Nishigaki Y, Nash WG, Stephens RM, Wang Y, de Jong PJ, O'Brien SJ, Yuhki N. Comparative feline genomics: a BAC/PAC contig map of the major histocompatibility complex class II region. Genomics 2001; 71:282-95. [PMID: 11170745 DOI: 10.1006/geno.2000.6416] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genome organization of the human major histocompatibility complex (MHC) will be best understood in a comparative evolutionary context. We describe here the construction of a physical map for the feline MHC. A large-insert domestic cat genomic DNA library was developed using a P1 artificial chromosome (PAC) with a genomic representation of 2.5x and an average insert size of 80 kb. A sequence-ready 660-kb bacterial artificial chromosome/PAC contig map of the domestic cat MHC class II region was constructed with a gene order similar to, but distinct from, that of human and mice: DPB/DPA, Ring3, DMB, TAP1, DOB, DRB2, DRA3, DRB1, DRA2, and DRA1. Fluorescence in situ hybridization analyses of selected class II PAC clones confirmed that the class II region lies in the pericentromeric region of cat chromosome B2. However, apparently unlike the human and mouse MHCs, the domestic cat DRA and DRB genes have undergone multiple duplications and the DQ region has been deleted.
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Affiliation(s)
- T W Beck
- Intramural Research Support Program, SAIC-Frederick, Frederick, Maryland 21702-1201, USA.
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