Gene content and virtual gene order of barley chromosome 1H

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

Research output: Contribution to journalArticlepeer-review

131 Scopus citations


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.

Original languageEnglish
Pages (from-to)496-505
Number of pages10
JournalPlant Physiology
Issue number2
StatePublished - Oct 2009
Externally publishedYes


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