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

被引：0

作者：

Sebastian Beier

Axel Himmelbach

Christian Colmsee

Xiao-Qi Zhang

Roberto A. Barrero

Qisen Zhang

Lin Li

Micha Bayer

Daniel Bolser

Stefan Taudien

Marco Groth

Marius Felder

Alex Hastie

Hana Šimková

Helena Staňková

Jan Vrána

Saki Chan

María Muñoz-Amatriaín

Rachid Ounit

Steve Wanamaker

Thomas Schmutzer

Lala Aliyeva-Schnorr

Stefano Grasso

Jaakko Tanskanen

Dharanya Sampath

Darren Heavens

Sujie Cao

Brett Chapman

Fei Dai

Yong Han

Hua Li

Xuan Li

Chongyun Lin

John K. McCooke

Cong Tan

Songbo Wang

Shuya Yin

Gaofeng Zhou

Jesse A. Poland

Matthew I. Bellgard

Andreas Houben

Jaroslav Doležel

Sarah Ayling

Stefano Lonardi

Peter Langridge

Gary J. Muehlbauer

Paul Kersey

Matthew D. Clark

Mario Caccamo

Alan H. Schulman

机构：

[1] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,Department of Agronomy and Plant Genetics

[2] School of Veterinary and Life Sciences,Department of Botany & Plant Sciences

[3] Murdoch University,Department of Computer Science and Engineering

[4] Centre for Comparative Genomics,Department of Agricultural and Environmental Sciences

[5] Murdoch University,Department of Plant Pathology and Department of Agronomy

[6] Australian Export Grains Innovation Centre,Department of Plant and Microbial Biology

[7] University of Minnesota,Department of Biology

[8] The James Hutton Institute,Department of Agriculture and Food

[9] European Molecular Biology Laboratory—The European Bioinformatics Institute,undefined

[10] Leibniz Institute on Aging—Fritz Lipmann Institute (FLI),undefined

[11] BioNano Genomics Inc.,undefined

[12] Institute of Experimental Botany,undefined

[13] Centre of the Region Haná for Biotechnological and Agricultural Research,undefined

[14] University of California,undefined

[15] Riverside,undefined

[16] University of California,undefined

[17] Riverside,undefined

[18] University of Udine,undefined

[19] Green Technology,undefined

[20] Natural Resources Institute (Luke),undefined

[21] Viikki Plant Science Centre,undefined

[22] and Institute of Biotechnology,undefined

[23] University of Helsinki,undefined

[24] Earlham Institute,undefined

[25] BGI-Shenzhen,undefined

[26] College of Agriculture and Biotechnology,undefined

[27] Zhejiang University,undefined

[28] Kansas State University,undefined

[29] Wheat Genetics Resource Center,undefined

[30] School of Agriculture,undefined

[31] University of Adelaide,undefined

[32] University of Minnesota,undefined

[33] School of Environmental Sciences,undefined

[34] University of East Anglia,undefined

[35] National Institute of Agricultural Botany,undefined

[36] Lund University,undefined

[37] Carlsberg Research Laboratory,undefined

[38] Government of Western Australia,undefined

[39] Hubei Collaborative Innovation Centre for Grain Industry,undefined

[40] Yangtze University,undefined

[41] School of Life Sciences,undefined

[42] University of Dundee,undefined

[43] School of Plant Biology,undefined

[44] University of Western Australia,undefined

[45] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig,undefined

来源：

Scientific Data | / 4卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

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).

引用

共 95 条

[1]

Schulte D(2009)The international barley sequencing consortium--at the threshold of efficient access to the barley genome Plant physiology 149 142-147

[2]

Schulte D(2011)BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L) BMC genomics 12 247-423

[3]

Ariyadasa R(2014)A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms Plant physiology 164 412-716

[4]

Mascher M(2012)A physical, genetic and functional sequence assembly of the barley genome Nature 491 711-727

[5]

Lander ES(2013)Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) The Plant Journal 76 718-921

[6]

Schnable PS(2001)Initial sequencing and analysis of the human genome Nature 409 860-1115

[7]

Lam ET(2009)The B73 maize genome: complexity, diversity, and dynamics Science 326 1112-776

[8]

Lieberman-Aiden E(2012)Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly Nature biotechnology 30 771-293

[9]

Burton JN(2009)Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 289-1125

[10]

Poland JA(2013)Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Nature biotechnology 31 1119-966

← 1 2 3 4 5 6 7 8 9 10 →