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      Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

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      1 , 1 , 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 8 , 8 , 9 , 10 , 10 , 10 , 9 , 11 , 12 , 11 , 1 , 1 , 13 , 14 , 15 , 15 , 16 , 3 , 17 , 17 , 16 , 16 , 16 , 3 , 3 , 16 , 17 , 2 , 18 , 3 , 1 , 10 , 15 , 12 , 19 , 5 , 20 , 7 , 15 , 21 , 15 , 22 , 14 , 8 , 11 , 23 , 17 , 24 , 2 , 25 , 26 , 6 , 27 , 1 , 1 , 28 , a , 1 , 29
      Scientific Data
      Nature Publishing Group
      DNA sequencing, Plant genetics, Genome assembly algorithms

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          Abstract

          Barley ( Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

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          Most cited references35

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Molecular Cloning : A Laboratory Manual

            <p>The first two editions of this manual have been mainstays of molecular biology for nearly twenty years, with an unrivalled reputation for reliability, accuracy, and clarity.<br>In this new edition, authors Joseph Sambrook and David Russell have completely updated the book, revising every protocol and adding a mass of new material, to broaden its scope and maintain its unbeatable value for studies in genetics, molecular cell biology, developmental biology, microbiology, neuroscience, and immunology.<br>Handsomely redesigned and presented in new bindings of proven durability, this three–volume work is essential for everyone using today’s biomolecular techniques.<br>The opening chapters describe essential techniques, some well–established, some new, that are used every day in the best laboratories for isolating, analyzing and cloning DNA molecules, both large and small.<br>These are followed by chapters on cDNA cloning and exon trapping, amplification of DNA, generation and use of nucleic acid probes, mutagenesis, and DNA sequencing.<br>The concluding chapters deal with methods to screen expression libraries, express cloned genes in both prokaryotes and eukaryotic cells, analyze transcripts and proteins, and detect protein–protein interactions.<br>The Appendix is a compendium of reagents, vectors, media, technical suppliers, kits, electronic resources and other essential information.<br>As in earlier editions, this is the only manual that explains how to achieve success in cloning and provides a wealth of information about why techniques work, how they were first developed, and how they have evolved. </p>
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              Shortest Connection Networks And Some Generalizations

              R. Prim (1957)
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                Author and article information

                Journal
                Sci Data
                Sci Data
                Scientific Data
                Nature Publishing Group
                2052-4463
                27 April 2017
                2017
                : 4
                : 170044
                Affiliations
                [1 ]Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , 06466 Seeland, Germany
                [2 ]School of Veterinary and Life Sciences, Murdoch University , Murdoch, Western Australia 6150, Australia
                [3 ]Centre for Comparative Genomics, Murdoch University , Murdoch, Western Australia 6150, Australia
                [4 ]Australian Export Grains Innovation Centre , South Perth, Western Australia 6151, Australia
                [5 ]Department of Agronomy and Plant Genetics, University of Minnesota , St Paul, Minnesota 55108, USA
                [6 ]The James Hutton Institute , Dundee DD2 5DA, UK
                [7 ]European Molecular Biology Laboratory—The European Bioinformatics Institute , Hinxton CB10 1SD, UK
                [8 ]Leibniz Institute on Aging—Fritz Lipmann Institute (FLI) , 07745 Jena, Germany
                [9 ]BioNano Genomics Inc. , San Diego, California 92121, USA
                [10 ]Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research , 78371 Olomouc, Czech Republic
                [11 ]Department of Botany & Plant Sciences, University of California, Riverside , Riverside, California 92521, USA
                [12 ]Department of Computer Science and Engineering, University of California, Riverside , Riverside, California 92521, USA
                [13 ]Department of Agricultural and Environmental Sciences, University of Udine , 33100 Udine, Italy
                [14 ]Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki , 00014 Helsinki, Finland
                [15 ]Earlham Institute , Norwich NR4 7UH, UK
                [16 ]BGI-Shenzhen , Shenzhen 518083, China
                [17 ]College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058, China
                [18 ]Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy , Manhattan, Kansas 66506, USA
                [19 ]School of Agriculture, University of Adelaide , Urrbrae, South Australia 5064, Australia
                [20 ]Department of Plant and Microbial Biology, University of Minnesota , St Paul, Minnesota 55108, USA
                [21 ]School of Environmental Sciences, University of East Anglia , Norwich NR4 7UH, UK
                [22 ]National Institute of Agricultural Botany , Cambridge CB3 0LE, UK
                [23 ]Department of Biology, Lund University , 22362 Lund, Sweden
                [24 ]Carlsberg Research Laboratory , 1799 Copenhagen, Denmark
                [25 ]Department of Agriculture and Food, Government of Western Australia , South Perth, Western Australia 6150, Australia
                [26 ]Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University , Jingzhou, Hubei 434025, China
                [27 ]School of Life Sciences, University of Dundee , Dundee DD2 5DA, UK
                [28 ]School of Plant Biology, University of Western Australia , Crawley 6009, Australia
                [29 ]German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , 04103 Leipzig, Germany
                Author notes
                [*]

                These authors contributed equally to this work

                []

                BAC sequencing and assembly (1H, 3H, 4H): S.B., A.Himmelbach, S.T., M.F., M.G., M.M., U.S. (co-leader), M.P. (co-leader), N.S. (leader); BAC sequencing and assembly (2H, unassigned): D.S., D.H., S.A. (co-leader), M.D.C. (co-leader), M.C. (co-leader), R.W. (leader); BAC sequencing and assembly (5H, 7H): X.Z., R.A.B., Q.Z., C.T., J.K.M., B.C., G.Zhou, F.D., Y.H., S.Y., S.Cao, S.Wang, X.L., M.I.B., P.L., G.Zhang (co-leader), C.Li (leader); BAC sequencing and assembly (6H): S.B., S.Wang, C.Lin, H.L., U.S., M.H. (co-leader), I.B. (leader); BAC sequencing (gene-bearing): M.M.-A., R.O., S.Wanamaker, S.L. (co-leader), T.J.C. (leader); Optical mapping: A.Hastie, H.Š., J.T., H.S., J.V., S.Chan, M.M., N.S., J.D., A.H.S. (leader); Chromosome conformation capture: A.Himmelbach, S.G., M.M. (co-leader), N.S. (leader); Pseudomolecule construction: M.M. (leader), S.B., C.C., D.B., T.S., P.K., N.S., U.S. (co-leader); Validation: L.L., M.B., L.A.-S., A.Houben, J.A.P., N.S., G.J.M., M.M. (leader). All authors read and commented on the manuscript.

                Author information
                http://orcid.org/0000-0002-2177-8781
                http://orcid.org/0000-0002-7735-665X
                http://orcid.org/0000-0003-0041-3115
                http://orcid.org/0000-0003-1073-6719
                http://orcid.org/0000-0002-6958-9912
                http://orcid.org/0000-0002-6263-0492
                http://orcid.org/0000-0002-4126-6177
                http://orcid.org/0000-0003-0596-8582
                http://orcid.org/0000-0003-1045-3065
                http://orcid.org/0000-0001-6113-3518
                http://orcid.org/0000-0003-3011-8731
                Article
                sdata201744
                10.1038/sdata.2017.44
                5407242
                28448065
                a608bd6c-e546-46a0-b30f-3330d7e0cfdd
                Copyright © 2017, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reuse.

                History
                : 26 August 2016
                : 09 February 2017
                Categories
                Data Descriptor

                dna sequencing,plant genetics,genome assembly algorithms

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