Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii.
BACKGROUND
Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.


RESULTS
We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein.


CONCLUSIONS
We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.
Moreira
Leandro M
LM
Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
Almeida
Nalvo F
NF
Potnis
Neha
N
Digiampietri
Luciano A
LA
Adi
Said S
SS
Bortolossi
Julio C
JC
da Silva
Ana C
AC
da Silva
Aline M
AM
de Moraes
Fabrício E
FE
de Oliveira
Julio C
JC
de Souza
Robson F
RF
Facincani
Agda P
AP
Ferraz
André L
AL
Ferro
Maria I
MI
Furlan
Luiz R
LR
Gimenez
Daniele F
DF
Jones
Jeffrey B
JB
Kitajima
Elliot W
EW
Laia
Marcelo L
ML
Leite
Rui P
RP
Nishiyama
Milton Y
MY
Rodrigues Neto
Julio
J
Nociti
Letícia A
LA
Norman
David J
DJ
Ostroski
Eric H
EH
Pereira
Haroldo A
HA
Staskawicz
Brian J
BJ
Tezza
Renata I
RI
Ferro
Jesus A
JA
Vinatzer
Boris A
BA
Setubal
João C
JC
D016960:Agrobacterium tumefaciens / Q000235:genetics; D018441:Biofilms; D002957:Citrus / Q000382:microbiology*; D005407:Flagella / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D005810:Multigene Family; D019081:O Antigens / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D053038:Quorum Sensing / Q000235:genetics; D043368:Ralstonia solanacearum / Q000235:genetics; D013045:Species Specificity; D014974:Xanthomonas / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000502:physiology
D019081:O Antigens; D010940:Plant Proteins
Mol Plant Microbe Interact. 2009 Jan;22(1):96-106
19061406
Annu Rev Phytopathol. 2004;42:385-414
15283671
Mol Gen Genet. 1991 May;226(3):409-17
1645442
Mol Plant Microbe Interact. 2009 Jun;22(6):747-57
19445599
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147
Annu Rev Phytopathol. 2004;42:163-84
15283664
Mol Plant Microbe Interact. 2007 Aug;20(8):934-43
17722697
Mol Biol Evol. 2000 Apr;17(4):540-52
10742046
Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16624-9
15545602
J Bacteriol. 2009 Jul;191(14):4534-45
19429624
FEMS Microbiol Lett. 2003 Feb 14;219(1):39-45
12594021
Mol Plant Microbe Interact. 2000 Sep;13(9):911-21
10975648
Mol Plant Microbe Interact. 1997 Sep;10(7):803-11
9304855
Appl Environ Microbiol. 2007 Mar;73(5):1612-21
17220258
Mol Genet Genomics. 2001 Sep;266(1):79-95
11589581
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10676-81
11526207
Nat Rev Microbiol. 2003 Nov;1(2):137-49
15035043
Appl Environ Microbiol. 2007 Jul;73(13):4379-84
17468277
Syst Appl Microbiol. 2006 Dec;29(8):690-5
17183629
J Bacteriol. 2005 Apr;187(7):2315-25
15774874
Genome Biol. 2004;5(2):R12
14759262
Biodegradation. 2008 Nov;19(6):831-9
18373236
Mol Plant Microbe Interact. 2005 Aug;18(8):856-68
16134898
Mol Gen Genet. 1990 Jun;222(1):157-60
1700268
Genome Res. 1998 Mar;8(3):195-202
9521923
Plant Dis. 2004 Nov;88(11):1179-1188
30795311
PLoS One. 2009;4(2):e4358
19194503
Int J Syst Evol Microbiol. 2010 Mar;60(Pt 3):515-525
19654364
Microbiology (Reading). 1999 Jan;145 ( Pt 1):197-209
10206699
Science. 2001 Dec 14;294(5550):2317-23
11743193
Mol Plant Microbe Interact. 2005 Jun;18(6):546-54
15986924
Mol Plant Microbe Interact. 2009 Jan;22(1):73-85
19061404
Nature. 2002 Jan 31;415(6871):497-502
11823852
Syst Appl Microbiol. 2008 Oct;31(5):366-77
18783906
BMC Bioinformatics. 2009 Jan 27;10:35
19173744
Mol Plant Microbe Interact. 1992 May-Jun;5(3):204-13
1421509
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
9862982
PLoS One. 2009 Aug 14;4(8):e6632
19680562
Microbiol Mol Biol Rev. 1999 Sep;63(3):523-53
10477307
Biol Met. 1991;4(1):41-7
1649616
J Bacteriol. 2002 Mar;184(5):1340-8
11844763
Microbiol Res. 2006;161(2):145-9
16427518
OMICS. 2005 Summer;9(2):160-72
15969648
J Bacteriol. 2004 Jan;186(2):543-55
14702323
Plant Cell. 2009 Apr;21(4):1305-23
19366901
Science. 2001 Dec 14;294(5550):2323-8
11743194
J Urol. 2007 Jan;177(1):365-8
17162092
FEMS Microbiol Rev. 2008 Aug;32(5):842-57
18557946
Nucleic Acids Res. 2001 Dec 15;29(24):5169-81
11812851
Nature. 2000 Jul 13;406(6792):151-9
10910347
Mol Microbiol. 2001 Sep;41(6):1271-81
11580833
BMC Microbiol. 2008 Jun 02;8:87
18518965
Plant J. 2005 Mar;41(6):801-14
15743446
Nucleic Acids Res. 2005 Jan 26;33(2):577-86
15673718
J Bacteriol. 2005 Aug;187(16):5560-7
16077100
Mol Plant Microbe Interact. 2007 Apr;20(4):346-57
17427805
Phytopathology. 2010 Mar;100(3):208-15
20128693
Microbiology (Reading). 2002 Jun;148(Pt 6):1637-1653
12055285
Nat Genet. 2004 Nov;36(11):1165-73
15467720
Microbiology (Reading). 2000 Apr;146 ( Pt 4):885-891
10784047
Genome Res. 1998 Mar;8(3):186-94
9521922
Syst Appl Microbiol. 2005 Aug;28(6):494-518
16104350
Mol Plant Microbe Interact. 2001 Jun;14(6):768-74
11386372
Genome Res. 2003 Sep;13(9):2178-89
12952885
Mol Microbiol. 1998 Jul;29(1):165-77
9701811
Bioinformatics. 2006 Sep 15;22(18):2196-203
16837528
Appl Environ Microbiol. 2007 Apr;73(8):2690-6
17293518
Gene. 2000 Jul 11;252(1-2):61-9
10903438
Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8
18039703
FEMS Microbiol Lett. 2001 Sep 25;203(2):165-71
11583843
Biotechnol Bioeng. 2006 Jan 5;93(1):188-200
16317765
Mol Plant Microbe Interact. 2000 Oct;13(10):1145-55
11043476
J Infect Dis. 2004 Aug 15;190(4):783-92
15272407
Appl Environ Microbiol. 2008 Sep;74(17):5579-82
18641157
Microbiology (Reading). 2007 Mar;153(Pt 3):719-726
17322192
Mol Microbiol. 1999 Nov;34(4):799-809
10564519
Genome Res. 2005 Jun;15(6):757-67
15899963
Infect Immun. 1989 Feb;57(2):303-13
2563254
J Bacteriol. 1990 Oct;172(10):5795-802
2170327
Mol Plant Pathol. 2009 Nov;10(6):749-66
19849782
J Plant Physiol. 2006 Feb;163(3):233-55
16386329
J Bacteriol. 2007 Oct;189(20):7507-10
17693510
Appl Biochem Biotechnol. 1999 Dec;82(3):175-83
15304770
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18631-6
19015524
BMC Microbiol. 2009 Jan 16;9:12
19149882
Bioinformatics. 2006 Nov 1;22(21):2688-90
16928733
J Microbiol Biotechnol. 2009 Feb;19(2):113-20
19307758
Science. 1996 Jul 19;273(5273):367-70
8662526
OMICS. 2005 Spring;9(1):43-76
15805778
PLoS Pathog. 2006 Oct;2(10):e104
17040127
Mol Plant Pathol. 2003 May 1;4(3):141-57
20569374
Nature. 2002 May 23;417(6887):459-63
12024217
Appl Environ Microbiol. 2002 Mar;68(3):1257-64
11872476
Nature. 1990 Jul 26;346(6282):385-6
2374611
Mol Plant Microbe Interact. 2007 Oct;20(10):1250-61
17918627
Plasmid. 2001 May;45(3):184-99
11407914
J Bacteriol. 1998 Apr;180(7):1607-17
9537354
Mol Plant Pathol. 2009 Mar;10(2):249-62
19236573
Genome Res. 1998 Mar;8(3):175-85
9521921
J Bacteriol. 2007 Jan;189(2):377-87
17085551
Microbiology (Reading). 2000 Sep;146 ( Pt 9):2229-2236
10974110
Appl Environ Microbiol. 1991 Sep;57(9):2724-30
16348555
Arch Microbiol. 1994;161(5):434-8
8042907
J Bacteriol. 2007 Nov;189(22):8277-89
17827286
Mol Plant Microbe Interact. 2005 Jan;18(1):33-42
15672816
Curr Opin Struct Biol. 2008 Apr;18(2):267-77
18249533
Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1737-42
14755059
Appl Environ Microbiol. 1994 Apr;60(4):1078-86
7912499
Curr Opin Microbiol. 2006 Apr;9(2):207-17
16529981
Mol Plant Pathol. 2004 Jan 1;5(1):1-15
20565577
Plant Dis. 2009 Oct;93(10):1074
30754357