title: BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.).
abstract: BACKGROUND
  Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place.
  
  
  RESULTS
  Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with <30 or >250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X.
  
  
  CONCLUSIONS
  BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.
authors: Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr, 3, 06466 Gatersleben, Germany.
authors: Daniela
authors: D
authors: Schulte
authors: Ruvini
authors: R
authors: Ariyadasa
authors: Bujun
authors: B
authors: Shi
authors: Delphine
authors: D
authors: Fleury
authors: Chris
authors: C
authors: Saski
authors: Michael
authors: M
authors: Atkins
authors: Pieter
authors: P
authors: deJong
authors: Cheng-Cang
authors: CC
authors: Wu
authors: Andreas
authors: A
authors: Graner
authors: Peter
authors: P
authors: Langridge
authors: Nils
authors: N
authors: Stein
references: Plant J. 2005 Jun;42(6):912-22
references: 15941403
references: Genome Res. 2000 Nov;10(11):1772-87
references: 11076862
references: Plant Physiol. 2009 Jan;149(1):142-7
references: 19126706
references: Genetics. 2001 Aug;158(4):1711-24
references: 11514457
references: BMC Genomics. 2005 Jun 09;6:89
references: 15946383
references: Nat Rev Genet. 2004 Aug;5(8):578-88
references: 15266340
references: Science. 2001 Feb 16;291(5507):1304-51
references: 11181995
references: PLoS Genet. 2009 Nov;5(11):e1000728
references: 19936048
references: Science. 2008 Oct 3;322(5898):101-4
references: 18832645
references: Biotechniques. 1997 Dec;23(6):978-82
references: 9421619
references: BMC Genomics. 2008 Jun 12;9:280
references: 18549474
references: Theor Appl Genet. 2003 Apr;106(6):1102-6
references: 12671759
references: Genome Res. 2006 Jan;16(1):140-7
references: 16344555
references: Theor Appl Genet. 2007 Mar;114(5):823-39
references: 17219208
references: Plant Methods. 2006 May 25;2:9
references: 16725032
references: PLoS Genet. 2009 Nov;5(11):e1000715
references: 19936061
references: Theor Appl Genet. 2004 Sep;109(5):1041-50
references: 15164176
references: Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1424-9
references: 17220272
references: BMC Genomics. 2008 Mar 25;9:139
references: 18366732
references: Genetics. 2003 Jun;164(2):673-83
references: 12807788
references: Science. 2009 Nov 20;326(5956):1112-5
references: 19965430
references: Nature. 2002 Aug 15;418(6899):743-50
references: 12181558
references: Nature. 2001 Feb 15;409(6822):934-41
references: 11237014
references: Theor Appl Genet. 2005 May;110(8):1363-71
references: 15834699
references: Nature. 2009 Jan 29;457(7229):551-6
references: 19189423
references: Nature. 2010 Feb 11;463(7282):763-8
references: 20148030
references: Plant Physiol. 2002 Aug;129(4):1781-7
references: 12177491
references: Theor Appl Genet. 2007 Aug;115(4):571-90
references: 17534593
references: Genomics. 1998 Aug 15;52(1):1-8
references: 9740665
references: Plant Physiol. 2002 Jan;128(1):9-12
references: 11788746
references: Methods Mol Biol. 2003;236:3-20
references: 14501055
references: Nucleic Acids Res. 1999 Sep 1;27(17):e13
references: 10446256
references: Plant Physiol. 2002 Dec;130(4):1686-96
references: 12481051
references: Funct Integr Genomics. 2005 Apr;5(2):97-103
references: 15666175
references: Nucleic Acids Res. 1994 Nov 25;22(23):4922-31
references: 7800481
references: Genome Biol. 2007;8(8):R165
references: 17697342
references: Nat Protoc. 2007;2(7):1661-74
references: 17641631
references: Genome Res. 2004 Feb;14(2):319-26
references: 14718376
references: Genome Res. 2000 Jan;10(1):129-36
references: 10645957
references: Genomics. 1995 Sep 20;29(2):413-25
references: 8666390
references: BMC Genomics. 2010 May 28;11:339
references: 20509895
references: Genomics. 2003 Sep;82(3):378-89
references: 12906862
references: Methods Enzymol. 1991;194:251-70
references: 2005791
references: Genomics. 1996 Jun 1;34(2):213-8
references: 8661051
references: Theor Appl Genet. 2005 Aug;111(4):630-9
references: 16049705
references: Cell. 1976 Sep;9(1):91-9
references: 788919
references: Plant J. 2004 Sep;39(6):960-8
references: 15341637
references: Genome Res. 1997 Nov;7(11):1072-84
references: 9371743