title: Gene content and virtual gene order of barley chromosome 1H.
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 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.
authors.affiliation: Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Mihaela
authors.initials: M
authors.lastname: Martis
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Pavla
authors.initials: P
authors.lastname: Suchánková
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.forename: Andreas
authors.initials: A
authors.lastname: Petzold
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Andreas
authors.initials: A
authors.lastname: Graner
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: 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
chemical_list: D005819:Genetic Markers
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: Theor Appl Genet. 2007 Mar;114(5):823-39
references.pmid: 17219208
references.citation: Curr Biol. 1995 Jul 1;5(7):737-9
references.pmid: 7583118
references.citation: Plant Physiol. 2001 Dec;127(4):1539-55
references.pmid: 11743099
references.citation: Nature. 2009 Jan 29;457(7229):551-6
references.pmid: 19189423
references.citation: Plant Physiol. 2009 Jan;149(1):142-7
references.pmid: 19126706
references.citation: Theor Appl Genet. 1994 Oct;89(2-3):240-8
references.pmid: 24177835
references.citation: Genomics. 1988 Apr;2(3):231-9
references.pmid: 3294162
references.citation: Chromosome Res. 2007;15(1):51-66
references.pmid: 17295126
references.citation: Trends Genet. 1993 Aug;9(8):259-61
references.pmid: 8379002
references.citation: BMC Genomics. 2008 Jun 19;9:294
references.pmid: 18565235
references.citation: Theor Appl Genet. 2006 Aug;113(4):651-9
references.pmid: 16810504
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6
references.pmid: 11959976
references.citation: Nucleic Acids Res. 2008 Jan;36(1):e5
references.pmid: 18084031
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1424-9
references.pmid: 17220272
references.citation: PLoS One. 2007 Dec 19;2(12):e1326
references.pmid: 18094749
references.citation: Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227-74
references.pmid: 6977
references.citation: BMC Genomics. 2006 Oct 26;7:275
references.pmid: 17067373
references.citation: Chromosome Res. 2007;15(1):21-31
references.pmid: 17295124
references.citation: Genetics. 2004 Oct;168(2):701-12
references.pmid: 15514046
references.citation: Nat Biotechnol. 2008 Oct;26(10):1135-45
references.pmid: 18846087
references.citation: Am J Pathol. 2004 Jan;164(1):23-33
references.pmid: 14695315
references.citation: Genome Res. 2003 May;13(5):954-64
references.pmid: 12695328
references.citation: BMC Genomics. 2008 Oct 31;9:518
references.pmid: 18976483
references.citation: Science. 2004 Mar 12;303(5664):1640-4
references.pmid: 15016992
references.citation: Plant J. 2006 Nov;48(3):463-74
references.pmid: 17010109
references.citation: Methods Mol Biol. 2008;439:1-18
references.pmid: 18370092
references.citation: Plant J. 2009 Sep;59(5):712-22
references.pmid: 19453446
references.citation: Science. 2008 Mar 7;319(5868):1333
references.pmid: 18323430
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Curr Opin Plant Biol. 2009 Apr;12(2):119-25
references.pmid: 19095493