Gene content and virtual gene order of barley chromosome 1H.
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.
Mayer
Klaus F X
KF
Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
Taudien
Stefan
S
Martis
Mihaela
M
Simková
Hana
H
Suchánková
Pavla
P
Gundlach
Heidrun
H
Wicker
Thomas
T
Petzold
Andreas
A
Felder
Marius
M
Steuernagel
Burkhard
B
Scholz
Uwe
U
Graner
Andreas
A
Platzer
Matthias
M
Dolezel
Jaroslav
J
Stein
Nils
N
D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005434:Flow Cytometry; D023061:Gene Order / Q000235:genetics*; D005818:Genetic Engineering; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics; D001467:Hordeum / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D045868:Sorghum / Q000235:genetics; D026801:Synteny / Q000235:genetics
D005819:Genetic Markers
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