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


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).

SUBMITTER: Beier S 

PROVIDER: S-EPMC5407242 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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

Beier Sebastian S   Himmelbach Axel A   Colmsee Christian C   Zhang Xiao-Qi XQ   Barrero Roberto A RA   Zhang Qisen Q   Li Lin L   Bayer Micha M   Bolser Daniel D   Taudien Stefan S   Groth Marco M   Felder Marius M   Hastie Alex A   Šimková Hana H   Staňková Helena H   Vrána Jan J   Chan Saki S   Muñoz-Amatriaín María M   Ounit Rachid R   Wanamaker Steve S   Schmutzer Thomas T   Aliyeva-Schnorr Lala L   Grasso Stefano S   Tanskanen Jaakko J   Sampath Dharanya D   Heavens Darren D   Cao Sujie S   Chapman Brett B   Dai Fei F   Han Yong Y   Li Hua H   Li Xuan X   Lin Chongyun C   McCooke John K JK   Tan Cong C   Wang Songbo S   Yin Shuya S   Zhou Gaofeng G   Poland Jesse A JA   Bellgard Matthew I MI   Houben Andreas A   Doležel Jaroslav J   Ayling Sarah S   Lonardi Stefano S   Langridge Peter P   Muehlbauer Gary J GJ   Kersey Paul P   Clark Matthew D MD   Caccamo Mario M   Schulman Alan H AH   Platzer Matthias M   Close Timothy J TJ   Hansson Mats M   Zhang Guoping G   Braumann Ilka I   Li Chengdao C   Waugh Robbie R   Scholz Uwe U   Stein Nils N   Mascher Martin M  

Scientific data 20170427


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 p  ...[more]

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2011-11-23 | GSE33773 | GEO