title: Fortunella margarita transcriptional reprogramming triggered by Xanthomonas citri subsp. citri.
abstract: BACKGROUND
  Citrus canker disease caused by the bacterial pathogen Xanthomonas citri subsp. citri (Xcc) has become endemic in areas where high temperature, rain, humidity, and windy conditions provide a favourable environment for the dissemination of the bacterium. Xcc is pathogenic on many commercial citrus varieties but appears to elicit an incompatible reaction on the citrus relative Fortunella margarita Swing (kumquat), in the form of a very distinct delayed necrotic response. We have developed subtractive libraries enriched in sequences expressed in kumquat leaves during both early and late stages of the disease. The isolated differentially expressed transcripts were subsequently sequenced. Our results demonstrate how the use of microarray expression profiling can help assign roles to previously uncharacterized genes and elucidate plant pathogenesis-response related mechanisms. This can be considered to be a case study in a citrus relative where high throughput technologies were utilized to understand defence mechanisms in Fortunella and citrus at the molecular level.
  
  
  RESULTS
  cDNAs from sequenced kumquat libraries (ESTs) made from subtracted RNA populations, healthy vs. infected, were used to make this microarray. Of 2054 selected genes on a customized array, 317 were differentially expressed (P < 0.05) in Xcc challenged kumquat plants compared to mock-inoculated ones. This study identified components of the incompatible interaction such as reactive oxygen species (ROS) and programmed cell death (PCD). Common defence mechanisms and a number of resistance genes were also identified. In addition, there were a considerable number of differentially regulated genes that had no homologues in the databases. This could be an indication of either a specialized set of genes employed by kumquat in response to canker disease or new defence mechanisms in citrus.
  
  
  CONCLUSIONS
  Functional categorization of kumquat Xcc-responsive genes revealed an enhanced defence-related metabolism as well as a number of resistant response-specific genes in the kumquat transcriptome in response to Xcc inoculation. Gene expression profile(s) were analyzed to assemble a comprehensive and inclusive image of the molecular interaction in the kumquat/Xcc system. This was done in order to elucidate molecular mechanisms associated with the development of the hypersensitive response phenotype in kumquat leaves. These data will be used to perform comparisons among citrus species to evaluate means to enhance the host immune responses against bacterial diseases.
authors.affiliation: Plant Molecular and Cellular Biology Program (PMCB), Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA. abeera@ufl.edu
authors.forename: Abeer A
authors.initials: AA
authors.lastname: Khalaf
authors.forename: Frederick G
authors.initials: FG
authors.lastname: Gmitter
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
authors.forename: Joaquin
authors.initials: J
authors.lastname: Dopazo
authors.forename: Gloria A
authors.initials: GA
authors.lastname: Moore
mesh_terms: D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D027821:Rutaceae / Q000235:genetics* / Q000382:microbiology; D059467:Transcriptome; D014974:Xanthomonas / Q000472:pathogenicity*
chemical_list: D018076:DNA, Complementary
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9323-8
references.pmid: 10900264
references.citation: Plant J. 2004 Sep;39(5):697-714
references.pmid: 15315633
references.citation: Protein Expr Purif. 2007 Jun;53(2):363-9
references.pmid: 17350859
references.citation: Methods Mol Biol. 2007;354:121-30
references.pmid: 17172750
references.citation: Plant J. 2000 Feb;21(4):393-9
references.pmid: 10758491
references.citation: Mol Plant Pathol. 2008 Sep;9(5):609-31
references.pmid: 19018992
references.citation: Mol Plant Microbe Interact. 2006 Mar;19(3):342-9
references.pmid: 16570663
references.citation: Plant J. 1998 Oct;16(2):223-33
references.pmid: 9839467
references.citation: Genome Biol. 2001;2(2):REVIEWS3004
references.pmid: 11182895
references.citation: Mol Plant Microbe Interact. 2004 Nov;17(11):1212-22
references.pmid: 15553246
references.citation: Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):16101-6
references.pmid: 14673096
references.citation: J Bacteriol. 2007 Apr;189(8):3271-9
references.pmid: 17293422
references.citation: Plant Sci. 2012 Apr;185-186:118-30
references.pmid: 22325873
references.citation: Int J Plant Genomics. 2008;2008:619832
references.pmid: 18483572
references.citation: Science. 2007 Oct 26;318(5850):648-51
references.pmid: 17962565
references.citation: Plant Physiol. 2011 May;156(1):213-27
references.pmid: 21398258
references.citation: Nat Cell Biol. 2000 Mar;2(3):E41-3
references.pmid: 10707095
references.citation: Plant Physiol. 2001 Feb;125(2):539-55
references.pmid: 11161012
references.citation: Biochem J. 1976 Jun 1;155(3):697-700
references.pmid: 182136
references.citation: Plant Cell. 2009 Aug;21(8):2473-84
references.pmid: 19684243
references.citation: FEBS Lett. 1994 Sep 26;352(2):159-62
references.pmid: 7925967
references.citation: Plant Cell. 1997 Feb;9(2):209-21
references.pmid: 9061952
references.citation: Plant Physiol. 2001 Sep;127(1):159-72
references.pmid: 11553744
references.citation: Cell Mol Biol Lett. 2003;8(3):809-24
references.pmid: 12949620
references.citation: Bioinformatics. 2006 May 1;22(9):1096-102
references.pmid: 16481333
references.citation: J Exp Bot. 2004 Mar;55(397):605-12
references.pmid: 14966215
references.citation: Plant J. 2006 Dec;48(5):784-95
references.pmid: 17092315
references.citation: Plant J. 1998 Apr;14(2):225-34
references.pmid: 9628018
references.citation: Bioessays. 2003 Jan;25(1):47-57
references.pmid: 12508282
references.citation: Plant Cell. 2006 Apr;18(4):1084-98
references.pmid: 16531496
references.citation: Nucleic Acids Res. 2008 Jun;36(10):3420-35
references.pmid: 18445632
references.citation: Semin Cell Dev Biol. 2010 Aug;21(6):550-7
references.pmid: 20044013
references.citation: Plant Physiol. 2003 Jun;132(2):999-1010
references.pmid: 12805628
references.citation: Plant Cell. 2003 Jan;15(1):165-78
references.pmid: 12509529
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2150-5
references.pmid: 9122163
references.citation: Science. 2007 Oct 26;318(5850):645-8
references.pmid: 17962564
references.citation: J Exp Bot. 2002 May;53(372):1227-36
references.pmid: 11997371
references.citation: Nucleic Acids Res. 2002 Feb 15;30(4):e15
references.pmid: 11842121
references.citation: Cell Host Microbe. 2008 Jun 12;3(6):348-51
references.pmid: 18541211
references.citation: Plant Cell. 1996 Oct;8(10):1683-1698
references.pmid: 12239358
references.citation: Plant Physiol. 2009 Apr;149(4):1797-809
references.pmid: 19176718
references.citation: Cell Mol Biol Lett. 2011 Mar;16(1):1-24
references.pmid: 20585889
references.citation: Bioinformatics. 2007 Jul 15;23(14):1792-800
references.pmid: 17519250
references.citation: Curr Biol. 2008 Sep 23;18(18):1396-401
references.pmid: 18771922
references.citation: New Phytol. 2008;178(3):503-14
references.pmid: 18346103
references.citation: Mol Plant. 2008 May;1(3):482-95
references.pmid: 19825555
references.citation: Mol Genet Genomics. 2008 Apr;279(4):415-27
references.pmid: 18247056
references.citation: Mol Plant Microbe Interact. 2004 Nov;17(11):1192-200
references.pmid: 15553245
references.citation: Cell. 2006 Aug 11;126(3):467-75
references.pmid: 16901781
references.citation: Plant Cell. 1998 Mar;10(3):371-82
references.pmid: 9501111
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S9
references.pmid: 19534758
references.citation: Int J Plant Genomics. 2008;2008:528361
references.pmid: 18509486
references.citation: Mol Biol Rep. 2006 Sep;33(3):223-31
references.pmid: 16850192
references.citation: Plant J. 1994 Apr;5(4):507-21
references.pmid: 8012404
references.citation: Plant Physiol. 2003 Aug;132(4):1901-12
references.pmid: 12913147
references.citation: Funct Integr Genomics. 2004 Jul;4(3):196-205
references.pmid: 14760538
references.citation: Plant Cell. 2005 Jul;17(7):1866-75
references.pmid: 15987996
references.citation: J Bacteriol. 1997 Sep;179(18):5655-62
references.pmid: 9294418
references.citation: Plant Biol (Stuttg). 2004 Jul;6(4):402-7
references.pmid: 15248122
references.citation: Plant J. 2005 Oct;44(1):139-54
references.pmid: 16167902
references.citation: Mol Plant Pathol. 2009 Nov;10(6):749-66
references.pmid: 19849782
references.citation: Plant Cell. 2001 Jan;13(1):163-78
references.pmid: 11158537
references.citation: Plant Physiol. 2004 Jan;134(1):420-31
references.pmid: 14701914
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18631-6
references.pmid: 19015524
references.citation: Physiol Plant. 2010 Apr;138(4):414-29
references.pmid: 20002601
references.citation: Mol Plant Microbe Interact. 2005 Feb;18(2):142-9
references.pmid: 15720083
references.citation: Trends Plant Sci. 2000 Jul;5(7):278-82
references.pmid: 10871899
references.citation: Science. 1998 Aug 28;281(5381):1309-12
references.pmid: 9721092
references.citation: Mol Plant Pathol. 2003 May 1;4(3):141-57
references.pmid: 20569374
references.citation: Nature. 2001 Jun 14;411(6839):843-7
references.pmid: 11459067
references.citation: Nature. 2006 Nov 16;444(7117):323-9
references.pmid: 17108957
references.citation: Planta. 2006 Dec;225(1):1-12
references.pmid: 16807755
references.citation: J Integr Plant Biol. 2010 Feb;52(2):195-204
references.pmid: 20377681
references.citation: Plant Cell. 2007 Mar;19(3):1081-95
references.pmid: 17384171