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GENOME ANALYSIS

Gene Content and Virtual Gene Order of Barley Chromosome 1H^{1,[C],[W],[OA]}

Klaus F.X. Mayer, Stefan Taudien, Mihaela Martis, Hana imková, Pavla Suchánková, Heidrun Gundlach, Thomas Wicker, Andreas Petzold, Marius Felder, Burkhard Steuernagel, Uwe Scholz, Andreas Graner, Matthias Platzer, Jaroslav Doleel and Nils Stein^*

Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M., M.M., H.G.); Leibniz Institute for Age Research, Fritz Lipmann Institute, 07745 Jena, Germany (S.T., A.P., M.F., M.P.); Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, 77200 Olomouc, Czech Republic (H.., P.S., J.D.); Institute of Plant Biology, University of Zurich, CH–8008 Zurich, Switzerland (T.W.); and Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (B.S., U.S., A.G., N.S.)

Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Nils Stein (stein{at}ipk-gatersleben.de).

^[C] Some figures in this article are displayed in color online but in black and white in the print edition.

^[W] The online version of this article contains Web-only data.

^[OA] Open access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.142612

^* Corresponding author; e-mail stein{at}ipk-gatersleben.de.

Received June 7, 2009; accepted August 13, 2009; published August 19, 2009.