Gene Content and Virtual Gene Order of Barley Chromosome 1H

Publication Type:Journal Article
Year of Publication:2009
Authors:Mayer, KEX, Taudien, S, Martis, M, Šimková, H, Suchánková, P, Gundlach, H, Wicker, T, Petzold, A, Felder, M, Steuernagel, B, Scholz, U, Graner, A, Platzer, M, Doležel, J, Stein, N
Journal:Plant Physiology
Volume:151
Issue:2
Date Published:2009
ISBN Number:00320889
Keywords:Hordeum, Hordeum vulgare, Oryza, Oryza sativa, Triticum
Abstract:

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 IH, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome IH 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, genie 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.

URL:http://www.jstor.org/stable/40537789
Short Title:Plant Physiology
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