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SRX006855: Gene content and virtual gene order of barley chromosome 1H - Titration run 1
1 LS454 (454 GS FLX) run: 12,462 spots, 3.3M bases, 6.9Mb downloads

Design: Intact mitotic chromosomes were isolated by flow cytometric sorting and the purity of the obtained chromosome suspension was determined by fluorescence in situ hybridization (FISH) essentially as described previously (Suchankova et al., 2006). The DNA of sorted chromosomes was purified and amplified by multiple displacement amplification (MDA) as described by Simkova et al. (Simkova et al., 2008).
Submitted by: Genome Analysis in the Biological System Plant (GABIPD)
Study: Gene content and virtual gene order of barley chromosome 1H
show Abstracthide Abstract
Chromosome 1H (ca 622 Mb) of barley (Hordeum vulgare L..) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization (FISH) 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 and sorghum and against wheat and barley EST 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. Syntenic relationships of chromosome 1H to rice chromosomes 5 and 10, and to sorghum chromosomes 1 and 9 were detected on a per gene resolution. Informed by the syntenic relationships to 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 EST datasets. Thus, integration of genomic, transcriptomic and synteny-derived information represents a major step towards developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.
Sample: Generic sample from Hordeum vulgare
SAMN00011084 • SRS000573 • All experiments • All runs
Organism: Hordeum vulgare
Name: WCA1H
Instrument: 454 GS FLX
Strategy: WCS
Selection: other
Layout: SINGLE
Spot descriptor:

Experiment attributes:
chromosome: 1H
Runs: 1 run, 12,462 spots, 3.3M bases, 6.9Mb
Run# of Spots# of BasesSizePublished


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