Genomic characterization and phylogenetic analysis of a narrow host-range Iranian strain of Xanthmonas citri sub. citri, NIGEB-88
Subject Areas : Plant MicrobiologyAmir Jalali 1 , Seyed Mehdi Alavi 2 , Mohammad Hossein Sangtarash 3
1 - Ph.D, Institute of Agriculture Biotechnology, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.
2 - Assistant Professor, Institute of Agriculture Biotechnology, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.
3 - Associate Professor, Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran.
Keywords: Xanthomonas citri subsp. citri, Citrus bacterial canker, Whole genome sequencing, A*-type,
Abstract :
Background & Objectives: Xanthomonas citri subsp. citri (Xcc) is the causal agent of citrus bacterial canker. In Iran, for the first time, Alizadeh and Rahimian reported the presence of Xcc on Mexican lime (C. aurantifolia), in 1990. Early characterization data suggested the presence of both wide (pathotype A) and narrow (pathotype A* and Aw) host range Xcc strains in Iran. However, more recently a discriminant analysis of MLVA-31 and MLVA-14 data in 2014 showed that Iranian strains of Xcc have genetically belonged to the host-restricted pathotype A* but not to the pathotype A. This study was aimed for genomic characterization and phylogenetic analysis of a narrow-host-rang Iranian strain of X. citri sub. citri, NIGEB-88.Materials & Methods: To determine genetic characteristics and phylogenetic relationships of Iranian strains, Illumina sequencing method was used to obtain a draft genome sequence of Xcc strain NIGEB-88.Results: General features of Iranian strain such as genome size, number of plasmids, average genomic GC content, number of CDS and structural RNA were similar to those of other Xcc pathotypes. Furthermore, studies of various potential virulence and host range determinants factors such as type III secretion system effectors, type IV secretion system and surface Lipopolysaccharides revealed that this pathogen is very close to XccA and XccAw strains.Conclusion: Phylogenetic and assessment of genes related to virulence and host specificity showed that XccA*NIGEB-88 is more closely related to other Iranian strain, XccA*NIGEB-386, and narrow-host-rang pathotype A*.
QC/E. According to the latest update in 2015
2. Ference CM, Gochez AM, Behlau F, Wang N, Graham JH, Jones JB. Recent advances in the
understanding of Xanthomonas citri ssp. citri pathogenesis and citrus canker disease
management. Mol Plant Pathol. 2017. doi: 10.1111/mpp.12638.
3. Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A.
Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiol. 2012; 12: 43.
4. Sun X, Stall RE, Jones JB, Cubero J, Gottwald TR, Graham JH, Dixon WH, Schubert TS,
Chaloux PH, Stromberg VK, Lacy GH and Sutton BD. Detection and characterization of a new
strain of citrus canker bacteria from key/Mexican lime and alemow in south Florida. Plant Dis.
2004; 88: 1179-1188.
5. Verniere C, Hartung JS, Pruvost OP, Civerolo EL, Alvarez AM, Maestri P and Luisetti J.
Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from
Southwest Asia. Eur J Plant Pathol. 1998; 104: 477-487.
6. Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O.
Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary
events giving rise to pathotypes with different host ranges. BMC Genomics. 2015; 16: 1098.
7. Piazza A, Zimaro T, Garavaglia BS, Ficarra FA, Thomas L, Marondedze C, Feil R, Lunn JE,
Gehring C, Ottado J, Gottig N. The dual nature of trehalose in citrus canker disease: a virulence
factor for Xanthomonas citri subsp. citri and a trigger for plant defence responses. J Exp Bot.
2015; 66(9): 2795-2811.
8. Alizadeh A, Rahimian H. Citrus canker in Kerman province. Iran J Plant Pathol. 1990; 26: 42.
9. Khodakaramian G, Rahimian H, Mohamadi M, Allameh A. Phenotypic characteristics, host
range and distribution of the strains of Xanthomonas axonopodis inducing citrus canker in
southern Iran. Iran J Plant Pathol. 1999; 35: 40-43.
10. Mohammadi M, Mirzaee MR, Rahimian H. Physiological and biochemical characteristics of
Iranian strains of Xanthomonas axonopodis pv. citri, the causal agent of citrus bacterial canker
disease. J Phytopath. 2001; 149: 65-75.
11. Khodakaramian G, Swings J. Genetic diversity and pathogenicity of Xanthomonas axonopodis
strains inducing citrus canker disease in Iran and South Korea. Indian J Microbiol. 2011; 51:
194-199.
12. Pruvost O, Goodarzi T, Boyer K, Soltaninejad H, Escalon A, Alavi SM, Javegny S, Boyer C,
Cottyn B, Gagnevin L and Vernière C. Genetic structure analysis of strains causing citrus
canker in Iran reveals the presence of two different lineages of Xanthomonas citri pv. citri
pathotype A*. Plant Pathol. 2015; 64(4): 776-784.
13. Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost
O, Arlat M, Gagnevin L. Variations in type III effector repertoires, pathological phenotypes
and host range of Xanthomonas citri pv. citri pathotypes. Mol Plant Pathol. 2013; 14(5):
483-496.
14. Jalali A, Alavi SM, Sangtarash MH. Comparative genomic analysis of wide and narrow host
range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of
their pathogenicity and virulence factors. Australasian Plant Pathol. 2017; 46(1): 49-61.
15. Desjardins P, Conklin D. NanoDrop microvolume quantitation of nucleic acids. J Vis Exp.
2010; 45: 2565.
16. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn
graphs. Genome Res. 2008; 18: 821-829.
17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze
A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic
Acids Res. 2016; 44(14): gkw569.
18. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ,
Brinkman FSL. PSORTb 3.0: Improved protein subcellular localization prediction with refined
localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;
26(13): 1608-1615.
19. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei
T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology
inference across 3686 organisms. Nucleic Acids Res. 2014; 42(D1): D231-D239.
20. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington
K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. The Pfam protein families database.
Nucleic Acids Res Database Issue. 2014; 42: D222-D230.
21. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst
Appl Microbiol. 2015; 38(4): 237-245.
22. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert
M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein
multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 11(7): 539.
23. Darling AE, Mau B, Perna NT. Progressive Mauve: multiple genome alignment with gene
gain, loss and rearrangement. PLoS One. 2010; 5(6): e11147.
24. Gao F, Zhang CT. GC-Profile: a web-based tool for visualizing and analyzing the variation of
GC content in genomic sequences. Nucleic Acids Res. 2006; 34: W686-W691
25. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes.
Nucleic Acids Res. 2008; 36: 181-184.
26. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for
bacterial insertion sequences. Nucleic Acids Research. 2006; 34: D32-D36.
27. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly
interspaced short palindromic repeats. Nucl Acids Res. 2007; 35: W52-W57.
28. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A,
Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A. Geneious Basic: an
integrated and extendable desktop software platform for the organization and analysis of
sequence data. Bioinformatics. 2012; 28(12): 1647-1649.
29. Frank AC, Lobry JR. Oriloc: prediction of replication boundaries in unannotated bacterial
chromosomes. Bioinformatics. 2000; 16: 560-561.
30. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial
innovation. Nature. 2000; 405: 299-304.
31. Midha S, Patil PB. Genomic insights into the evolutionary origin of Xanthomonas
axonopodis pv. citri and its ecological relatives. Appl Environ Microbiol. 2014; 80(20):
6266-6279.
32. Al-Saadi A, Reddy JD, Duan YP, Brunings AM, Yuan Q, Gabriel DW. All five host-range
variants of Xanthomonas citri carry one pthA homolog with 17.5 repeats that determines
pathogenicity on citrus, but none determine host-range variation. Mol Plant Microbe Interact.
2007; 20: 934-943.
33. Desvaux M, Hebraud M, Henderson IR, Pallen MJ. Type III secretion: what’s in a name?
Trends Microbiol. 2006; 14(4): 157-160.
34. Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N.
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp.
citri provide insights into mechanisms of bacterial virulence and host range. BMC Genomics.
2013; 14: 551.
_||_
QC/E. According to the latest update in 2015
2. Ference CM, Gochez AM, Behlau F, Wang N, Graham JH, Jones JB. Recent advances in the
understanding of Xanthomonas citri ssp. citri pathogenesis and citrus canker disease
management. Mol Plant Pathol. 2017. doi: 10.1111/mpp.12638.
3. Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A.
Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiol. 2012; 12: 43.
4. Sun X, Stall RE, Jones JB, Cubero J, Gottwald TR, Graham JH, Dixon WH, Schubert TS,
Chaloux PH, Stromberg VK, Lacy GH and Sutton BD. Detection and characterization of a new
strain of citrus canker bacteria from key/Mexican lime and alemow in south Florida. Plant Dis.
2004; 88: 1179-1188.
5. Verniere C, Hartung JS, Pruvost OP, Civerolo EL, Alvarez AM, Maestri P and Luisetti J.
Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from
Southwest Asia. Eur J Plant Pathol. 1998; 104: 477-487.
6. Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O.
Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary
events giving rise to pathotypes with different host ranges. BMC Genomics. 2015; 16: 1098.
7. Piazza A, Zimaro T, Garavaglia BS, Ficarra FA, Thomas L, Marondedze C, Feil R, Lunn JE,
Gehring C, Ottado J, Gottig N. The dual nature of trehalose in citrus canker disease: a virulence
factor for Xanthomonas citri subsp. citri and a trigger for plant defence responses. J Exp Bot.
2015; 66(9): 2795-2811.
8. Alizadeh A, Rahimian H. Citrus canker in Kerman province. Iran J Plant Pathol. 1990; 26: 42.
9. Khodakaramian G, Rahimian H, Mohamadi M, Allameh A. Phenotypic characteristics, host
range and distribution of the strains of Xanthomonas axonopodis inducing citrus canker in
southern Iran. Iran J Plant Pathol. 1999; 35: 40-43.
10. Mohammadi M, Mirzaee MR, Rahimian H. Physiological and biochemical characteristics of
Iranian strains of Xanthomonas axonopodis pv. citri, the causal agent of citrus bacterial canker
disease. J Phytopath. 2001; 149: 65-75.
11. Khodakaramian G, Swings J. Genetic diversity and pathogenicity of Xanthomonas axonopodis
strains inducing citrus canker disease in Iran and South Korea. Indian J Microbiol. 2011; 51:
194-199.
12. Pruvost O, Goodarzi T, Boyer K, Soltaninejad H, Escalon A, Alavi SM, Javegny S, Boyer C,
Cottyn B, Gagnevin L and Vernière C. Genetic structure analysis of strains causing citrus
canker in Iran reveals the presence of two different lineages of Xanthomonas citri pv. citri
pathotype A*. Plant Pathol. 2015; 64(4): 776-784.
13. Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost
O, Arlat M, Gagnevin L. Variations in type III effector repertoires, pathological phenotypes
and host range of Xanthomonas citri pv. citri pathotypes. Mol Plant Pathol. 2013; 14(5):
483-496.
14. Jalali A, Alavi SM, Sangtarash MH. Comparative genomic analysis of wide and narrow host
range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of
their pathogenicity and virulence factors. Australasian Plant Pathol. 2017; 46(1): 49-61.
15. Desjardins P, Conklin D. NanoDrop microvolume quantitation of nucleic acids. J Vis Exp.
2010; 45: 2565.
16. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn
graphs. Genome Res. 2008; 18: 821-829.
17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze
A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic
Acids Res. 2016; 44(14): gkw569.
18. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ,
Brinkman FSL. PSORTb 3.0: Improved protein subcellular localization prediction with refined
localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;
26(13): 1608-1615.
19. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei
T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology
inference across 3686 organisms. Nucleic Acids Res. 2014; 42(D1): D231-D239.
20. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington
K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. The Pfam protein families database.
Nucleic Acids Res Database Issue. 2014; 42: D222-D230.
21. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst
Appl Microbiol. 2015; 38(4): 237-245.
22. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert
M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein
multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 11(7): 539.
23. Darling AE, Mau B, Perna NT. Progressive Mauve: multiple genome alignment with gene
gain, loss and rearrangement. PLoS One. 2010; 5(6): e11147.
24. Gao F, Zhang CT. GC-Profile: a web-based tool for visualizing and analyzing the variation of
GC content in genomic sequences. Nucleic Acids Res. 2006; 34: W686-W691
25. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes.
Nucleic Acids Res. 2008; 36: 181-184.
26. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for
bacterial insertion sequences. Nucleic Acids Research. 2006; 34: D32-D36.
27. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly
interspaced short palindromic repeats. Nucl Acids Res. 2007; 35: W52-W57.
28. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A,
Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A. Geneious Basic: an
integrated and extendable desktop software platform for the organization and analysis of
sequence data. Bioinformatics. 2012; 28(12): 1647-1649.
29. Frank AC, Lobry JR. Oriloc: prediction of replication boundaries in unannotated bacterial
chromosomes. Bioinformatics. 2000; 16: 560-561.
30. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial
innovation. Nature. 2000; 405: 299-304.
31. Midha S, Patil PB. Genomic insights into the evolutionary origin of Xanthomonas
axonopodis pv. citri and its ecological relatives. Appl Environ Microbiol. 2014; 80(20):
6266-6279.
32. Al-Saadi A, Reddy JD, Duan YP, Brunings AM, Yuan Q, Gabriel DW. All five host-range
variants of Xanthomonas citri carry one pthA homolog with 17.5 repeats that determines
pathogenicity on citrus, but none determine host-range variation. Mol Plant Microbe Interact.
2007; 20: 934-943.
33. Desvaux M, Hebraud M, Henderson IR, Pallen MJ. Type III secretion: what’s in a name?
Trends Microbiol. 2006; 14(4): 157-160.
34. Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N.
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp.
citri provide insights into mechanisms of bacterial virulence and host range. BMC Genomics.
2013; 14: 551.