title: Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences.
abstract: BACKGROUND
  Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina), one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement.
  
  
  RESULTS
  Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES) of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome) and estimation of gene content (31,000 genes) of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus.
  
  
  CONCLUSIONS
  In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest. Paired end sequences also may be very helpful for whole-genome sequencing programs.
authors.affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, Km. 4,5 Moncada, Valencia, E46113, Spain. terol_javalc@gva.es
authors.forename: Javier
authors.initials: J
authors.lastname: Terol
authors.forename: M Angel
authors.initials: MA
authors.lastname: Naranjo
authors.forename: Patrick
authors.initials: P
authors.lastname: Ollitrault
authors.forename: Manuel
authors.initials: M
authors.lastname: Talon
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D002957:Citrus / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant
chemical_list: D018744:DNA, Plant
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):229-33
references.pmid: 12519988
references.citation: Planta. 2007 Sep;226(4):989-1005
references.pmid: 17541628
references.citation: Genome Res. 2004 Feb;14(2):319-26
references.pmid: 14718376
references.citation: Theor Appl Genet. 2006 May;112(7):1248-57
references.pmid: 16474971
references.citation: Theor Appl Genet. 2003 Mar;106(5):826-36
references.pmid: 12647056
references.citation: Theor Appl Genet. 2006 Jul;113(2):239-50
references.pmid: 16791690
references.citation: Genetics. 2006 Apr;172(4):2541-55
references.pmid: 16489220
references.citation: BMC Genomics. 2007;8:31
references.pmid: 17254327
references.citation: Nat Genet. 1997 Jan;15(1):57-61
references.pmid: 8988169
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Plant Physiol. 2002 Dec;130(4):1686-96
references.pmid: 12481051
references.citation: Genome Res. 1998 Mar;8(3):186-94
references.pmid: 9521922
references.citation: Curr Opin Plant Biol. 2002 Apr;5(2):94-100
references.pmid: 11856602
references.citation: Theor Appl Genet. 2007 Apr;114(6):1081-90
references.pmid: 17287974
references.citation: Theor Appl Genet. 2002 Nov;105(6-7):1058-1066
references.pmid: 12582934
references.citation: Genome. 2007 Sep;50(9):871-5
references.pmid: 17893728
references.citation: J Exp Bot. 2007;58(6):1407-20
references.pmid: 17317673
references.citation: Yi Chuan Xue Bao. 2006 Apr;33(4):345-53
references.pmid: 16625833
references.citation: Theor Appl Genet. 2006 May;112(8):1519-31
references.pmid: 16699791
references.citation: Genetics. 2001 Nov;159(3):1231-42
references.pmid: 11729165
references.citation: Theor Appl Genet. 2005 Aug;111(3):456-66
references.pmid: 15942755
references.citation: Plant Mol Biol. 2005 Feb;57(3):375-91
references.pmid: 15830128
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Genetics. 2006 May;173(1):151-61
references.pmid: 16547112
references.citation: Genome. 2001 Aug;44(4):572-81
references.pmid: 11550890
references.citation: Genomics. 2004 Dec;84(6):941-51
references.pmid: 15533711
references.citation: PLoS One. 2007;2(12):e1326
references.pmid: 18094749
references.citation: BMC Plant Biol. 2007;7:29
references.pmid: 17562019
references.citation: Theor Appl Genet. 2004 May;108(8):1627-34
references.pmid: 15235775
references.citation: Mol Cells. 2006 Dec 31;22(3):300-7
references.pmid: 17202858
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: J Mol Evol. 1998 Jan;46(1):45-53
references.pmid: 9419224
references.citation: Nat Genet. 1999 Dec;23(4):452-6
references.pmid: 10581034
references.citation: Science. 2006 Sep 15;313(5793):1596-604
references.pmid: 16973872
references.citation: Genome Res. 2002 Oct;12(10):1611-8
references.pmid: 12368254
references.citation: Genomics. 2007 May;89(5):630-7
references.pmid: 17270394
references.citation: Methods Mol Biol. 2004;256:1-6
references.pmid: 15024155
references.citation: Theor Appl Genet. 2003 Sep;107(5):931-9
references.pmid: 12830387
references.citation: Plant Cell Rep. 2003 Aug;22(1):59-63
references.pmid: 12835994
references.citation: Proc Biol Sci. 2001 Nov 7;268(1482):2211-20
references.pmid: 11674868
references.citation: Plant Mol Biol. 2006 Nov;62(4-5):513-27
references.pmid: 16897468
references.citation: Mol Genet Genomics. 2006 May;275(5):479-91
references.pmid: 16501995
references.citation: Mol Genet Genomics. 2007 Apr;277(4):365-77
references.pmid: 17216224
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: J Agric Food Chem. 2006 Jun 28;54(13):4888-95
references.pmid: 16787044
references.citation: Genome Res. 2004 Dec;14(12):2439-47
references.pmid: 15574823
references.citation: Theor Appl Genet. 2003 Dec;108(1):121-30
references.pmid: 12937896
references.citation: BMC Plant Biol. 2006;6:21
references.pmid: 17010212
references.citation: J Agric Food Chem. 2007 Oct 31;55(22):9047-53
references.pmid: 17910511
references.citation: BMC Genomics. 2006;7:174
references.pmid: 16824208
references.citation: Int J Plant Genomics. 2008;2008:528361
references.pmid: 18509486
references.citation: Mol Genet Genomics. 2006 Jul;276(1):1-12
references.pmid: 16703363
references.citation: Genome Res. 1999 Sep;9(9):868-77
references.pmid: 10508846
references.citation: Plant Cell. 2002 Mar;14(3):537-45
references.pmid: 11910002
references.citation: Genome. 2001 Jun;44(3):382-93
references.pmid: 11444697
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507