Differences

This shows you the differences between two versions of the page.

--- refnotes:refnotes [2020/02/11 23:08]
jfpothier
+++ refnotes:refnotes [2020/04/06 17:34] (current)
bosis
@@ Line 3: / Line 3: @@
 ====== Overview ======
-This page is supposed to hold all citations used anywhere in the Dokuwiki. It is supposed to be divided into sections if appropriate. Enter records in [[http://www.bibtex.org/Format/|bibtex]] format between tags. Citation can be included at any page by typing<code>
+This page is supposed to hold all citations used anywhere in the Dokuwiki. It is supposed to be divided into sections if appropriate. Enter records in [[http://www.bibtex.org/Format/|bibtex]] format between tags. Citation can be included at any page by typing
+<code>
 [(:euroxanth:name)]
@@ Line 9: / Line 10: @@
 </code>
-where ''"name"'' is the identifier of the citation in the bibtex record. Please use ''":cite:"'' namespace everywhere and use folowing self-explanatory scheme for citation ''"name"'': ''authorYEARfirst_unique_words_of_title''. E.g.:
+where ''"name"'' is the identifier of the citation in the bibtex record. Please use ''":euroxanth:"'' namespace everywhere and use following self-explanatory scheme for citation ''"name"'': ''authorYEARfirst_unique_words_of_title''. E.g.:
 <code>
 @Comment{refnotes,
   namespace = ":euroxanth"
 }
-@Book{Blank2005four,
+@Book{Blank2005,
     url="http://www.amazon.co.uk/Four-Steps-Epiphany-Steven-Blank/dp/0976470705",
     published="2005",
@@ Line 20: / Line 21: @@
     authors="Blank, S.G."
 }
-@Misc{Doe1999something,
+@Misc{Doe1999,
     url="http://example.com",
     published="1999",
-    title="Somethong happened to me",
+    title="Something happened to me",
     authors="Doe, J."
 }
 </code>
-You should allways specify the first author. If you are uncertain in year, use underscore instead, e.g. srinivasan_engineering, but don't forget to specify enough words (separated by underscores), to obtain a unique identifier.
+You should always specify the first author. If you are uncertain in year, use underscore instead, e.g. Srinivasan_engineering, but don't forget to specify enough words (separated by underscores), to obtain a unique identifier.
 See [[https://www.dokuwiki.org/plugin:refnotes:syntax|refnotes plugin]] documentation for further details.
+====== Bib entry from DOI ======
+If you happen to know the DOI of a publication and want to obtain a bib entry, go to the [[http://www.doi2bib.org/#/doi|doi2bib service]] and type in your DOI.
 ====== Type 3 effectors publications ======
@@ Line 49: / Line 53: @@
   year      = 2005,
   pages     = "7254-7266",
-  pages     = "10.1128/JB.187.21.7254-7266.2005",
+  doi       = "10.1128/JB.187.21.7254-7266.2005",
   url       = "https://dx.doi.org/10.1128%2FJB.187.21.7254-7266.2005"
 }
@@ Line 62: / Line 66: @@
   pages     = "634-636",
   url       = "https://www.apsnet.org/publications/phytopathology/backissues/Documents/1979Articles/Phyto69n06_634.PDF"
+}
+@article{RN70,
+  author    = "Astua-Monge, Gustavo and Minsavage, Gerald V. and Stall, Robert E. and Davis, Michael J. and Bonas, Ulla and Jones, Jeffrey B.",
+  ref-author= "RN70",
+  title     = "Resistance of Tomato and Pepper to T3 Strains of Xanthomonas campestris pv. Vesicatoria Is Specified by a Plant-Inducible Avirulence Gene",
+  journal   = "Molecular Plant-Microbe Interactions",
+  volume    = "13",
+  number    = "9",
+  pages     = "911-921",
+  DOI       = "10.1094/mpmi.2000.13.9.911",
+  url       = "https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.2000.13.9.911",
+  year      = "2000",
+  type      = "Journal Article"
+}
+@article{RN80,
+author = {Bahadur, Ranjit Prasad and Basak, Jolly},
+title = {Molecular modeling of protein-protein interaction to decipher the structural mechanism of nonhost resistance in rice},
+journal = {Journal of biomolecular structure & dynamics},
+volume = {32},
+number = {4},
+pages = {669-681},
+ISSN = {0739-1102},
+DOI = {10.1080/07391102.2013.787370},
+url = {http://europepmc.org/abstract/MED/23659345
+https://doi.org/10.1080/07391102.2013.787370},
+year = {2014},
+type = {Journal Article}
+}
+@article{RN88,
+author = {Barak, Jeri D. and Vancheva, Taca and Lefeuvre, Pierre and Jones, Jeffrey B. and Timilsina, Sujan and Minsavage, Gerald V. and Vallad, Gary E. and Koebnik, Ralf},
+title = {Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors},
+journal = {Frontiers in Plant Science},
+volume = {7},
+number = {1805},
+ISSN = {1664-462X},
+DOI = {10.3389/fpls.2016.01805},
+url = {https://www.frontiersin.org/article/10.3389/fpls.2016.01805},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN48,
+author = {Boch, Jens and Bonas, Ulla},
+title = {Xanthomonas AvrBs3 Family-Type III Effectors: Discovery and Function},
+journal = {Annual Review of Phytopathology},
+volume = {48},
+number = {1},
+pages = {419-436},
+DOI = {10.1146/annurev-phyto-080508-081936},
+url = {https://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-080508-081936},
+year = {2010},
+type = {Journal Article}
+}
+@article{RN31,
+author = {Boch, Jens and Scholze, Heidi and Schornack, Sebastian and Landgraf, Angelika and Hahn, Simone and Kay, Sabine and Lahaye, Thomas and Nickstadt, Anja and Bonas, Ulla},
+title = {Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors},
+journal = {Science},
+volume = {326},
+number = {5959},
+pages = {1509-1512},
+DOI = {10.1126/science.1178811},
+url = {https://science.sciencemag.org/content/sci/326/5959/1509.full.pdf},
+year = {2009},
+type = {Journal Article}
+}
+@article{RN94,
+author = {Bocsanczy, A. M. and Schneider, D. J. and DeClerck, G. A. and Cartinhour, S. and Beer, S. V.},
+title = {HopX1 in Erwinia amylovora Functions as an Avirulence Protein in Apple and Is Regulated by HrpL},
+journal = {Journal of Bacteriology},
+volume = {194},
+number = {3},
+pages = {553-560},
+DOI = {10.1128/jb.05065-11},
+url = {https://jb.asm.org/content/jb/194/3/553.full.pdf},
+year = {2012},
+type = {Journal Article}
+}
+@article{RN92,
+author = {Bogdanove, Adam J. and Koebnik, Ralf and Lu, Hong and Furutani, Ayako and Angiuoli, Samuel V. and Patil, Prabhu B. and Van Sluys, Marie-Anne and Ryan, Robert P. and Meyer, Damien F. and Han, Sang-Wook and Aparna, Gudlur and Rajaram, Misha and Delcher, Arthur L. and Phillippy, Adam M. and Puiu, Daniela and Schatz, Michael C. and Shumway, Martin and Sommer, Daniel D. and Trapnell, Cole and Benahmed, Faiza and Dimitrov, George and Madupu, Ramana and Radune, Diana and Sullivan, Steven and Jha, Gopaljee and Ishihara, Hiromichi and Lee, Sang-Won and Pandey, Alok and Sharma, Vikas and Sriariyanun, Malinee and Szurek, Boris and Vera-Cruz, Casiana M. and Dorman, Karin S. and Ronald, Pamela C. and Verdier, Valérie and Dow, J. Maxwell and Sonti, Ramesh V. and Tsuge, Seiji and Brendel, Volker P. and Rabinowicz, Pablo D. and Leach, Jan E. and White, Frank F. and Salzberg, Steven L.},
+title = {Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic <span class="named-content genus-species" id="named-content-1">Xanthomonas</span> spp},
+journal = {Journal of Bacteriology},
+volume = {193},
+number = {19},
+pages = {5450-5464},
+DOI = {10.1128/jb.05262-11},
+url = {https://jb.asm.org/content/jb/193/19/5450.full.pdf},
+year = {2011},
+type = {Journal Article}
+}
+@article{RN25,
+author = {Bonas, Ulla and Schulte, Ralf and Fenselau, Stefan and Minsavage, Gerald V. and Staskawicz, Brian J. and Stall, Robert E.},
+title = {Isolation of a Gene Cluster from Xanthomonas campestris pv. vesicatoria that Determines Pathogenicity and the Hypersensitive Response on Pepper and Tomato},
+journal = {Molecular Plant-Microbe Interactions},
+volume = {4},
+pages = {81-88},
+DOI = {10.1094/MPMI-4-081},
+year = {1991},
+type = {Journal Article}
+}
+@article{RN24,
+author = {Bonas, Ulla and Stall, Robert E. and Staskawicz, Brian},
+title = {Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria},
+journal = {Molecular and General Genetics MGG},
+volume = {218},
+number = {1},
+pages = {127-136},
+ISSN = {1432-1874},
+DOI = {10.1007/BF00330575},
+url = {https://doi.org/10.1007/BF00330575},
+year = {1989},
+type = {Journal Article}
+}
+@article{RN27,
+author = {Bonas, Ulla and Van den Ackerveken, Guido},
+title = {Gene-for-gene interactions: bacterial avirulence proteins specify plant disease resistance},
+journal = {Current Opinion in Microbiology},
+volume = {2},
+number = {1},
+pages = {94-98},
+ISSN = {1369-5274},
+DOI = {10.1016/S1369-5274(99)80016-2},
+url = {http://www.sciencedirect.com/science/article/pii/S1369527499800162},
+year = {1999},
+type = {Journal Article}
+}
+@article{RN41,
+author = {Büttner, Daniela},
+title = {Behind the lines–actions of bacterial type III effector proteins in plant cells},
+journal = {FEMS Microbiology Reviews},
+volume = {40},
+number = {6},
+pages = {894-937},
+ISSN = {0168-6445},
+DOI = {10.1093/femsre/fuw026},
+url = {https://doi.org/10.1093/femsre/fuw026},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN49,
+author = {Büttner, Daniela and Bonas, Ulla},
+title = {Regulation and secretion of Xanthomonas virulence factors},
+journal = {FEMS Microbiology Reviews},
+volume = {34},
+number = {2},
+pages = {107-133},
+ISSN = {0168-6445},
+DOI = {10.1111/j.1574-6976.2009.00192.x},
+url = {https://doi.org/10.1111/j.1574-6976.2009.00192.x},
+year = {2010},
+type = {Journal Article}
+}
+@article{RN14,
+author = {Casper-Lindley, Catharina and Dahlbeck, Douglas and Clark, Eszter T. and Staskawicz, Brian J.},
+title = {Direct biochemical evidence for type III secretion-dependent translocation of the AvrBs2 effector protein into plant cells},
+journal = {Proceedings of the National Academy of Sciences},
+volume = {99},
+number = {12},
+pages = {8336-8341},
+DOI = {10.1073/pnas.122220299},
+url = {https://www.pnas.org/content/pnas/99/12/8336.full.pdf},
+year = {2002},
+type = {Journal Article}
+}
+@article{RN74,
+author = {Castañeda, Adriana and Reddy, Joseph D. and El-Yacoubi, Basma and Gabriel, Dean W.},
+title = {Mutagenesis of all Eight avr Genes in Xanthomonas campestris pv. campestris Had No Detected Effect on Pathogenicity, But One avr Gene Affected Race Specificity},
+journal = {Molecular Plant-Microbe Interactions},
+volume = {18},
+number = {12},
+pages = {1306-1317},
+DOI = {10.1094/mpmi-18-1306},
+url = {https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-18-1306},
+year = {2005},
+type = {Journal Article}
+}
+@article{RN53,
+author = {Cerutti, Aude and Jauneau, Alain and Auriac, Marie-Christine and Lauber, Emmanuelle and Martinez, Yves and Chiarenza, Serge and Leonhardt, Nathalie and Berthomé, Richard and Noel, Laurent D.},
+title = {Immunity at cauliflower hydathodes controls infection by Xanthomonas campestris pv. campestris},
+journal = {Plant Physiology},
+pages = {pp.01852.2016},
+DOI = {10.1104/pp.16.01852},
+url = {http://www.plantphysiol.org/content/plantphysiol/early/2017/02/09/pp.16.01852.full.pdf},
+year = {2017},
+type = {Journal Article}
+}
+@article{RN21,
+author = {Coplin, David L.},
+title = {Plasmids and Their Role in the Evolution of Plant Pathogenic Bacteria},
+journal = {Annual Review of Phytopathology},
+volume = {27},
+number = {1},
+pages = {187-212},
+DOI = {10.1146/annurev.py.27.090189.001155},
+url = {https://www.annualreviews.org/doi/abs/10.1146/annurev.py.27.090189.001155},
+year = {1989},
+type = {Journal Article}
+}
+@article{RN1,
+author = {Dahlbeck, D. and Stall, R.E.},
+title = {Mutations for Change of Race in Cultures of Xanthomonas vesicatoria},
+journal = {Phytopathology},
+volume = {69},
+pages = {634-636},
+DOI = {10.1094/Phyto-69-634},
+year = {1979},
+type = {Journal Article}
+}
+@article{RN97,
+author = {Dalio, Ronaldo J. D. and Magalhães, Diogo M. and Rodrigues, Carolina M. and Arena, Gabriella D. and Oliveira, Tiago S. and Souza-Neto, Reinaldo R. and Picchi, Simone C. and Martins, Paula M. M. and Santos, Paulo J. C. and Maximo, Heros J. and Pacheco, Inaiara S. and De Souza, Alessandra A. and Machado, Marcos A.},
+title = {PAMPs, PRRs, effectors and R-genes associated with citrus–pathogen interactions},
+journal = {Annals of Botany},
+volume = {119},
+number = {5},
+pages = {749-774},
+ISSN = {0305-7364},
+DOI = {10.1093/aob/mcw238},
+url = {https://doi.org/10.1093/aob/mcw238},
+year = {2017},
+type = {Journal Article}
+}
+@article{RN46,
+author = {Dean, Paul},
+title = {Functional domains and motifs of bacterial type III effector proteins and their roles in infection},
+journal = {FEMS Microbiology Reviews},
+volume = {35},
+number = {6},
+pages = {1100-1125},
+ISSN = {0168-6445},
+DOI = {10.1111/j.1574-6976.2011.00271.x},
+url = {https://doi.org/10.1111/j.1574-6976.2011.00271.x},
+year = {2011},
+type = {Journal Article}
+}
+@article{RN44,
+author = {Doyle, Erin L. and Stoddard, Barry L. and Voytas, Daniel F. and Bogdanove, Adam J.},
+title = {TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins},
+journal = {Trends in Cell Biology},
+volume = {23},
+number = {8},
+pages = {390-398},
+ISSN = {0962-8924},
+DOI = {https://doi.org/10.1016/j.tcb.2013.04.003},
+url = {http://www.sciencedirect.com/science/article/pii/S0962892413000573},
+year = {2013},
+type = {Journal Article}
+}
+@article{RN59,
+author = {Escalon, Aline and Javegny, Stéphanie and Vernière, Christian and Noël, Laurent D. and Vital, Karine and Poussier, Stéphane and Hajri, Ahmed and Boureau, Tristan and Pruvost, Olivier and Arlat, Matthieu and Gagnevin, Lionel},
+title = {Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes},
+journal = {Molecular Plant Pathology},
+volume = {14},
+number = {5},
+pages = {483-496},
+ISSN = {1464-6722},
+DOI = {10.1111/mpp.12019},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12019},
+year = {2013},
+type = {Journal Article}
+}
+@article{RN2,
+author = {Escolar, Lucia and Van Den Ackerveken, Guido and Pieplow, Sylvia and Rossier, Ombeline and Bonas, Ulla},
+title = {Type III secretion and in planta recognition of the Xanthomonas avirulence proteins AvrBs1 and AvrBsT},
+journal = {Molecular Plant Pathology},
+volume = {2},
+number = {5},
+pages = {287-296},
+ISSN = {1464-6722},
+DOI = {10.1046/j.1464-6722.2001.00077.x},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1464-6722.2001.00077.x},
+year = {2001},
+type = {Journal Article}
+}
+@article{RN55,
+author = {Feng, Feng and Yang, Fan and Rong, Wei and Wu, Xiaogang and Zhang, Jie and Chen, She and He, Chaozu and Zhou, Jian-Min},
+title = {A Xanthomonas uridine 5′-monophosphate transferase inhibits plant immune kinases},
+journal = {Nature},
+volume = {485},
+number = {7396},
+pages = {114-118},
+ISSN = {1476-4687},
+DOI = {10.1038/nature10962},
+url = {https://doi.org/10.1038/nature10962},
+year = {2012},
+type = {Journal Article}
+}
+@article{RN99,
+author = {Ferreira, Marisa A. S. V. and Bonneau, Sophie and Briand, Martial and Cesbron, Sophie and Portier, Perrine and Darrasse, Armelle and Gama, Marco A. S. and Barbosa, Maria Angélica G. and Mariano, Rosa de L. R. and Souza, Elineide B. and Jacques, Marie-Agnès},
+title = {Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen},
+journal = {Frontiers in Plant Science},
+volume = {10},
+number = {489},
+ISSN = {1664-462X},
+DOI = {10.3389/fpls.2019.00489},
+url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00489},
+year = {2019},
+type = {Journal Article}
+}
+@phdthesis{RN107,
+author = {Garita-Cambronero, J},
+title = {Genómica comparativa de cepas de Xanthomonas arborícola asociadas a Prunus ssp. Caracterización de los procesos de infección de la mancha bacteriana de frutales de hueso y almendro},
+university = {Universidad Politécnica de Madrid},
+year = {2016},
+type = {Thesis}
+}
+@article{RN101,
+author = {Garita-Cambronero, Jerson and Palacio-Bielsa, Ana and Cubero, Jaime},
+title = {Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context},
+journal = {Molecular Plant Pathology},
+volume = {19},
+number = {9},
+pages = {2053-2065},
+ISSN = {1464-6722},
+DOI = {10.1111/mpp.12679},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12679},
+year = {2018},
+type = {Journal Article}
+}
+@article{RN102,
+author = {Garita-Cambronero, Jerson and Palacio-Bielsa, Ana and López, María M. and Cubero, Jaime},
+title = {Comparative Genomic and Phenotypic Characterization of Pathogenic and Non-Pathogenic Strains of Xanthomonas arboricola Reveals Insights into the Infection Process of Bacterial Spot Disease of Stone Fruits},
+journal = {PLOS ONE},
+volume = {11},
+number = {8},
+pages = {e0161977},
+DOI = {10.1371/journal.pone.0161977},
+url = {https://doi.org/10.1371/journal.pone.0161977},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN100,
+author = {Garita-Cambronero, Jerson and Sena-Vélez, Marta and Ferragud, Elisa and Sabuquillo, Pilar and Redondo, Cristina and Cubero, Jaime},
+title = {Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants},
+journal = {PLOS ONE},
+volume = {14},
+number = {7},
+pages = {e0219797},
+DOI = {10.1371/journal.pone.0219797},
+url = {https://doi.org/10.1371/journal.pone.0219797},
+year = {2019},
+type = {Journal Article}
+}
+@article{RN3,
+author = {Gürlebeck, Doreen and Jahn, Simone and Gürlebeck, Norman and Szczesny, Robert and Szurek, Boris and Hahn, Simone and Hause, Gerd and Bonas, Ulla},
+title = {Visualization of novel virulence activities of the Xanthomonas type III effectors AvrBs1, AvrBs3 and AvrBs4},
+journal = {Molecular Plant Pathology},
+volume = {10},
+number = {2},
+pages = {175-188},
+ISSN = {1464-6722},
+DOI = {10.1111/j.1364-3703.2008.00519.x},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1364-3703.2008.00519.x},
+year = {2009},
+type = {Journal Article}
+}
+@article{RN35,
+author = {Gürlebeck, Doreen and Szurek, Boris and Bonas, Ulla},
+title = {Dimerization of the bacterial effector protein AvrBs3 in the plant cell cytoplasm prior to nuclear import},
+journal = {The Plant Journal},
+volume = {42},
+number = {2},
+pages = {175-187},
+ISSN = {0960-7412},
+DOI = {10.1111/j.1365-313X.2005.02370.x},
+url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02370.x},
+year = {2005},
+type = {Journal Article}
+}
+@article{RN57,
+author = {Guy, Endrick and Genissel, Anne and Hajri, Ahmed and Chabannes, Matthieu and David, Perrine and Carrere, Sébastien and Lautier, Martine and Roux, Brice and Boureau, Tristan and Arlat, Matthieu and Poussier, Stéphane and Noël, Laurent D.},
+title = {Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity on Arabidopsis Revealed by Association and Reverse Genetics},
+journal = {mBio},
+volume = {4},
+number = {3},
+pages = {e00538-12},
+DOI = {10.1128/mBio.00538-12},
+url = {https://mbio.asm.org/content/mbio/4/3/e00538-12.full.pdf},
+year = {2013},
+type = {Journal Article}
+}
+@article{RN54,
+author = {Guy, Endrick and Lautier, Martine and Chabannes, Matthieu and Roux, Brice and Lauber, Emmanuelle and Arlat, Matthieu and Noël, Laurent D.},
+title = {xopAC-triggered Immunity against Xanthomonas Depends on Arabidopsis Receptor-Like Cytoplasmic Kinase Genes PBL2 and RIPK},
+journal = {PLOS ONE},
+volume = {8},
+number = {8},
+pages = {e73469},
+DOI = {10.1371/journal.pone.0073469},
+url = {https://doi.org/10.1371/journal.pone.0073469},
+year = {2013},
+type = {Journal Article}
+}
+@article{RN83,
+author = {Han, Qian and Zhou, Changhe and Wu, Shuchi and Liu, Yi and Triplett, Lindsay and Miao, Jiamin and Tokuhisa, James and Deblais, Loïc and Robinson, Howard and Leach, Jan E and Li, Jianyong and Zhao, Bingyu},
+title = {Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2},
+journal = {Structure},
+volume = {23},
+number = {10},
+pages = {1900-1909},
+ISSN = {0969-2126},
+DOI = {https://doi.org/10.1016/j.str.2015.06.030},
+url = {http://www.sciencedirect.com/science/article/pii/S0969212615003251},
+year = {2015},
+type = {Journal Article}
+}
+@article{RN60,
+author = {Harrison, James and Studholme, David J.},
+title = {Draft genome sequence of Xanthomonas axonopodis pathovar vasculorum NCPPB 900},
+journal = {FEMS Microbiology Letters},
+volume = {360},
+number = {2},
+pages = {113-116},
+ISSN = {0378-1097},
+DOI = {10.1111/1574-6968.12607},
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+author = {Roux, Brice and Bolot, Stéphanie and Guy, Endrick and Denancé, Nicolas and Lautier, Martine and Jardinaud, Marie-Françoise and Fischer-Le Saux, Marion and Portier, Perrine and Jacques, Marie-Agnès and Gagnevin, Lionel and Pruvost, Olivier and Lauber, Emmanuelle and Arlat, Matthieu and Carrère, Sébastien and Koebnik, Ralf and Noël, Laurent D.},
+title = {Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome},
+journal = {BMC Genomics},
+volume = {16},
+number = {1},
+pages = {975},
+ISSN = {1471-2164},
+DOI = {10.1186/s12864-015-2190-0},
+url = {https://doi.org/10.1186/s12864-015-2190-0},
+year = {2015},
+type = {Journal Article}
+}
+@article{RN78,
+author = {Salomon, Dor and Dar, Daniel and Sreeramulu, Shivakumar and Sessa, Guido},
+title = {Expression of Xanthomonas campestris pv. vesicatoria Type III Effectors in Yeast Affects Cell Growth and Viability},
+journal = {Molecular Plant-Microbe Interactions},
+volume = {24},
+number = {3},
+pages = {305-314},
+DOI = {10.1094/mpmi-09-10-0196},
+url = {https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-09-10-0196},
+year = {2011},
+type = {Journal Article}
+}
+@article{RN47,
+author = {Scholze, Heidi and Boch, Jens},
+title = {TAL effectors are remote controls for gene activation},
+journal = {Current Opinion in Microbiology},
+volume = {14},
+number = {1},
+pages = {47-53},
+ISSN = {1369-5274},
+DOI = {https://doi.org/10.1016/j.mib.2010.12.001},
+url = {http://www.sciencedirect.com/science/article/pii/S1369527410001888},
+year = {2011},
+type = {Journal Article}
+}
+@article{RN85,
+author = {Schuebel, Felix and Rocker, Andrea and Edelmann, Daniel and Schessner, Julia and Brieke, Clara and Meinhart, Anton},
+title = {3′-NADP and 3′-NAADP, Two Metabolites Formed by the Bacterial Type III Effector AvrRxo1},
+journal = {Journal of Biological Chemistry},
+volume = {291},
+number = {44},
+pages = {22868-22880},
+DOI = {10.1074/jbc.M116.751297},
+url = {http://www.jbc.org/content/291/44/22868.abstract},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN98,
+author = {Schwartz, Allison R. and Potnis, Neha and Timilsina, Sujan and Wilson, Mark and Patané, José and Martins, Joaquim and Minsavage, Gerald V. and Dahlbeck, Douglas and Akhunova, Alina and Almeida, Nalvo and Vallad, Gary E. and Barak, Jeri D. and White, Frank F. and Miller, Sally A. and Ritchie, David and Goss, Erica and Bart, Rebecca S. and Setubal, João C. and Jones, Jeffrey B. and Staskawicz, Brian J.},
+title = {Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity},
+journal = {Frontiers in Microbiology},
+volume = {6},
+number = {535},
+ISSN = {1664-302X},
+DOI = {10.3389/fmicb.2015.00535},
+url = {https://www.frontiersin.org/article/10.3389/fmicb.2015.00535},
+year = {2015},
+type = {Journal Article}
+}
+@article{RN86,
+author = {Shidore, Teja and Broeckling, Corey D. and Kirkwood, Jay S. and Long, John J. and Miao, Jiamin and Zhao, Bingyu and Leach, Jan E. and Triplett, Lindsay R.},
+title = {The effector AvrRxo1 phosphorylates NAD in planta},
+journal = {PLOS Pathogens},
+volume = {13},
+number = {6},
+pages = {e1006442},
+DOI = {10.1371/journal.ppat.1006442},
+url = {https://doi.org/10.1371/journal.ppat.1006442},
+year = {2017},
+type = {Journal Article}
+}
+@article{RN8,
+author = {Stall, Robert E. and Loschke, David C. and Jones, Jeffrey B},
+title = {Linkage of copper resistance and avirulence loci on a self-transmissible plasmid in Xanthomonas campestris pv. vesicatoria},
+journal = {Molecular Plant Pathology },
+volume = {76},
+pages = {240-243},
+DOI = {10.1094/Phyto-76-240},
+year = {1986},
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+}
+@article{RN23,
+author = {Stella, Stefano and Molina, Rafael and Yefimenko, Igor and Prieto, Jesus and Silva, George and Bertonati, Claudia and Juillerat, Alexandre and Duchateau, Phillippe and Montoya, Guillermo},
+title = {Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism},
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+}
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+title = {Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt},
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+}
+@article{RN9,
+author = {Swanson, J. and Kearney, B. and Dahlbeck, D. and Staskawicz, B.},
+title = {Cloned avirulence gene of Xanthomonas campestris pv. vesicatoria complements spontaneous race-change mutants},
+journal = {Molecular Plant-Microbe Interactions},
+volume = {1},
+number = {1},
+pages = {5-9},
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+}
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+author = {Szczesny, Robert and Büttner, Daniela and Escolar, Lucia and Schulze, Sebastian and Seiferth, Anja and Bonas, Ulla},
+title = {Suppression of the AvrBs1-specific hypersensitive response by the YopJ effector homolog AvrBsT from Xanthomonas depends on a SNF1-related kinase},
+journal = {New Phytologist},
+volume = {187},
+number = {4},
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+}
+@article{RN29,
+author = {Szurek, Boris and Rossier, Ombeline and Hause, Gerd and Bonas, Ulla},
+title = {Type III-dependent translocation of the Xanthomonas AvrBs3 protein into the plant cell},
+journal = {Molecular Microbiology},
+volume = {46},
+number = {1},
+pages = {13-23},
+ISSN = {0950-382X},
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+}
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+author = {Teper, Doron and Burstein, David and Salomon, Dor and Gershovitz, Michael and Pupko, Tal and Sessa, Guido},
+ref-author = {Teper et al.},
+title = {Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach},
+journal = {Molecular Plant Pathology},
+volume = {17},
+number = {3},
+pages = {398-411},
+ISSN = {1464-6722},
+DOI = {10.1111/mpp.12288},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12288},
+year = {2016},
+type = {Journal Article}
+}
+@article{teper2018xanthomonas,
+  title={The Xanthomonas euvesicatoria type III effector XopAU is an active protein kinase that manipulates plant MAP kinase signaling},
+  author={Teper, Doron and Girija, Anil Madhusoodana and Bosis, Eran and Popov, Georgy and Savidor, Alon and Sessa, Guido},
+  ref-author={Teper et al. 2018},
+  journal={PLoS pathogens},
+  volume={14},
+  number={1},
+  pages={e1006880},
+  year={2018},
+  publisher={Public Library of Science}
+}
+@article{RN11,
+author = {Teper, Doron and Sunitha, Sukumaran and Martin, Gregory B. and Sessa, Guido},
+title = {Five Xanthomonas type III effectors suppress cell death induced by components of immunity-associated MAP kinase cascades},
+journal = {Plant Signaling & Behavior},
+volume = {10},
+number = {10},
+pages = {e1064573},
+ISSN = {null},
+DOI = {10.1080/15592324.2015.1064573},
+url = {https://doi.org/10.1080/15592324.2015.1064573},
+year = {2015},
+type = {Journal Article}
+}
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+author = {Thieme, Frank and Koebnik, Ralf and Bekel, Thomas and Berger, Carolin and Boch, Jens and Büttner, Daniela and Caldana, Camila and Gaigalat, Lars and Goesmann, Alexander and Kay, Sabine and Kirchner, Oliver and Lanz, Christa and Linke, Burkhard and McHardy, Alice C. and Meyer, Folker and Mittenhuber, Gerhard and Nies, Dietrich H. and Niesbach-Klösgen, Ulla and Patschkowski, Thomas and Rückert, Christian and Rupp, Oliver and Schneiker, Susanne and Schuster, Stephan C. and Vorhölter, Frank-Jörg and Weber, Ernst and Pühler, Alfred and Bonas, Ulla and Bartels, Daniela and Kaiser, Olaf},
+title = {Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence},
+journal = {Journal of Bacteriology},
+volume = {187},
+number = {21},
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+}
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+title = {AvrRxo1 Is a Bifunctional Type III Secreted Effector and Toxin-Antitoxin System Component with Homologs in Diverse Environmental Contexts},
+journal = {PLOS ONE},
+volume = {11},
+number = {7},
+pages = {e0158856},
+DOI = {10.1371/journal.pone.0158856},
+url = {https://doi.org/10.1371/journal.pone.0158856},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN26,
+author = {Van den Ackerveken, Guido and Marois, Eric and Bonas, Ulla},
+title = {Recognition of the Bacterial Avirulence Protein AvrBs3 Occurs inside the Host Plant Cell},
+journal = {Cell},
+volume = {87},
+number = {7},
+pages = {1307-1316},
+ISSN = {0092-8674},
+DOI = {10.1016/S0092-8674(00)81825-5},
+url = {http://www.sciencedirect.com/science/article/pii/S0092867400818255},
+year = {1996},
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+}
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+author = {Vicente, Joana G. and Rothwell, Steve and Holub, Eric B. and Studholme, David J.},
+title = {Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida},
+journal = {International Journal of Systematic and Evolutionary Microbiology},
+volume = {67},
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+ISSN = {1466-5026},
+DOI = {https://doi.org/10.1099/ijsem.0.002189},
+url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002189},
+year = {2017},
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+}
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+title = {The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis},
+journal = {Journal of Biotechnology},
+volume = {134},
+number = {1},
+pages = {33-45},
+ISSN = {0168-1656},
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+}
+@article{RN56,
+author = {Wang, Guoxun and Roux, Brice and Feng, Feng and Guy, Endrick and Li, Lin and Li, Nannan and Zhang, Xiaojuan and Lautier, Martine and Jardinaud, Marie-Françoise and Chabannes, Matthieu and Arlat, Matthieu and Chen, She and He, Chaozu and Noël, Laurent D and Zhou, Jian-Min},
+title = {The Decoy Substrate of a Pathogen Effector and a Pseudokinase Specify Pathogen-Induced Modified-Self Recognition and Immunity in Plants},
+journal = {Cell Host & Microbe},
+volume = {18},
+number = {3},
+pages = {285-295},
+ISSN = {1931-3128},
+DOI = {https://doi.org/10.1016/j.chom.2015.08.004},
+url = {http://www.sciencedirect.com/science/article/pii/S1931312815003327},
+year = {2015},
+type = {Journal Article}
+}
+@article{RN73,
+author = {Wang, Lifeng and Tang, Xiaoyan and He, Chaozu},
+title = {The bifunctional effector AvrXccC of Xanthomonas campestris pv. campestris requires plasma membrane-anchoring for host recognition},
+journal = {Molecular Plant Pathology},
+volume = {8},
+number = {4},
+pages = {491-501},
+ISSN = {1464-6722},
+DOI = {10.1111/j.1364-3703.2007.00409.x},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1364-3703.2007.00409.x},
+year = {2007},
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+}
+@article{RN71,
+author = {Washington, Erica J. and Mukhtar, M. Shahid and Finkel, Omri M. and Wan, Li and Banfield, Mark J. and Kieber, Joseph J. and Dangl, Jeffery L.},
+title = {Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction},
+journal = {Proceedings of the National Academy of Sciences},
+volume = {113},
+number = {25},
+pages = {E3577-E3586},
+DOI = {10.1073/pnas.1606322113},
+url = {https://www.pnas.org/content/pnas/113/25/E3577.full.pdf},
+year = {2016},
+type = {Journal Article}
+}
+@article{RN61,
+author = {Wasukira, Arthur and Tayebwa, Johnbosco and Thwaites, Richard and Paszkiewicz, Konrad and Aritua, Valente and Kubiriba, Jerome and Smith, Julian and Grant, Murray and Studholme, David J.},
+title = {Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum},
+journal = {Genes},
+volume = {3},
+number = {3},
+pages = {361-377},
+ISSN = {2073-4425},
+url = {https://www.mdpi.com/2073-4425/3/3/361},
+year = {2012},
+type = {Journal Article}
+}
+@article{RN15,
+author = {Wei, Chudan and Ding, Tian and Chang, Changqing and Yu, Chengpeng and Li, Xingwei and Liu, Qiongguang},
+title = {Global Regulator PhoP is Necessary for Motility, Biofilm Formation, Exoenzyme Production, and Virulence of Xanthomonas citri Subsp. citri on Citrus Plants},
+journal = {Genes},
+volume = {10},
+number = {5},
+pages = {340},
+ISSN = {2073-4425},
+DOI = {10.3390/genes10050340},
+url = {https://www.mdpi.com/2073-4425/10/5/340},
+year = {2019},
+type = {Journal Article}
+}
+@article{RN51,
+author = {White, Frank F. and Potnis, Neha and Jones, Jeffrey B. and Koebnik, Ralf},
+title = {The type III effectors of Xanthomonas},
+journal = {Molecular Plant Pathology},
+volume = {10},
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+pages = {749-766},
+ISSN = {1464-6722},
+DOI = {10.1111/j.1364-3703.2009.00590.x},
+url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1364-3703.2009.00590.x},
+year = {2009},
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+}
+@article{RN79,
+author = {Wonni, I. and Cottyn, B. and Detemmerman, L. and Dao, S. and Ouedraogo, L. and Sarra, S. and Tekete, C. and Poussier, S. and Corral, R. and Triplett, L. and Koita, O. and Koebnik, R. and Leach, J. and Szurek, B. and Maes, M. and Verdier, V.},
+title = {Analysis of Xanthomonas oryzae pv. oryzicola Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity},
+journal = {Phytopathology},
+volume = {104},
+number = {5},
+pages = {520-531},
+DOI = {10.1094/phyto-07-13-0213-r},
+url = {https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-07-13-0213-R},
+year = {2014},
+type = {Journal Article}
+}
+@article{RN77,
+author = {Xie, Xue-Wen and Yu, Jing and Xu, Jian-Long and Zhou, Yong-Li and Li, Zhi-Kang},
+title = {Introduction of A Nonhost Gene Rxo1 Cloned from Maize Resistant to Rice Bacterial Leaf Streak into Rice Varieties},
+journal = {Chinese Journal of Biotechnology},
+volume = {23},
+number = {4},
+pages = {607-611},
+ISSN = {1872-2075},
+DOI = {https://doi.org/10.1016/S1872-2075(07)60039-9},
+url = {http://www.sciencedirect.com/science/article/pii/S1872207507600399},
+year = {2007},
+type = {Journal Article}
+}
+@article{RN52,
+author = {Xu, Rong-Qi and Blanvillain, Servane and Feng, Jia-Xun and Jiang, Bo-Le and Li, Xian-Zhen and Wei, Hong-Yu and Kroj, Thomas and Lauber, Emmanuelle and Roby, Dominique and Chen, Baoshan and He, Yong-Qiang and Lu, Guang-Tao and Tang, Dong-Jie and Vasse, Jacques and Arlat, Matthieu and Tang, Ji-Liang},
+title = {AvrACXcc8004, a Type III Effector with a Leucine-Rich Repeat Domain from Xanthomonas campestris Pathovar campestris Confers Avirulence in Vascular Tissues of Arabidopsis thaliana Ecotype Col-0},
+journal = {Journal of Bacteriology},
+volume = {190},
+number = {1},
+pages = {343-355},
+DOI = {10.1128/jb.00978-07},
+url = {https://jb.asm.org/content/jb/190/1/343.full.pdf},
+year = {2008},
+type = {Journal Article}
+}
+@article{RN75,
+author = {Zhao, Bingyu and Ardales, Edna Y. and Raymundo, Asuncion and Bai, Jianfa and Trick, Harold N. and Leach, Jan E. and Hulbert, Scot H.},
+title = {The avrRxo1 Gene from the Rice Pathogen Xanthomonas oryzae pv. oryzicola Confers a Nonhost Defense Reaction on Maize with Resistance Gene Rxo1},
+journal = {Molecular Plant-Microbe Interactions},
+volume = {17},
+number = {7},
+pages = {771-779},
+DOI = {10.1094/mpmi.2004.17.7.771},
+url = {https://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.2004.17.7.771},
+year = {2004},
+type = {Journal Article}
+}
+@article{RN17,
+author = {Zhao, Bingyu and Dahlbeck, Douglas and Krasileva, Ksenia V. and Fong, Richard W. and Staskawicz, Brian J.},
+title = {Computational and Biochemical Analysis of the Xanthomonas Effector AvrBs2 and Its Role in the Modulation of Xanthomonas Type Three Effector Delivery},
+journal = {PLoS Pathogens},
+volume = {7},
+number = {12},
+pages = {e1002408},
+DOI = {10.1371/journal.ppat.1002408},
+url = {https://doi.org/10.1371/journal.ppat.1002408},
+year = {2011},
+type = {Journal Article}
+}
+@article{RN76,
+author = {Zhao, Bingyu and Lin, Xinghua and Poland, Jesse and Trick, Harold and Leach, Jan and Hulbert, Scot},
+title = {A maize resistance gene functions against bacterial streak disease in rice},
+journal = {Proceedings of the National Academy of Sciences},
+volume = {102},
+number = {43},
+pages = {15383-15388},
+DOI = {10.1073/pnas.0503023102},
+url = {https://www.pnas.org/content/pnas/102/43/15383.full.pdf},
+year = {2005},
+type = {Journal Article}
 }
@@ Line 91: / Line 1501: @@
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 avrbs2
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+  - Casper-Lindley C. Dahlbeck D, Clark ET, Staskawicz BJ (2002). Direct biochemical evidence for type III secretion-dependent translocation of the AvrBs2 effector protein into plant cells. //Proceedings of the National Academy of Sciences//, //99//  (12), 8336-8341. doi: [[https://doi.org/10.1073/pnas.122220299|10.1073/pnas.122220299]]
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@@ Line 393: / Line 1803: @@
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@@ Line 416: / Line 1826: @@
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+  - de Feyter, R., McFadden, H., & Dennis, L. (1998). Five avirulence genes from Xanthomonas campestris pv. malvacearum cause genotype-specific cell death when expressed transiently in cotton. //Molecular plant-microbe interactions//, //11//  (7), 698-701
-  - Essenberg, M., Bayles, M. B., Samad, R. A., Hall, J. A., Brinkerhoff, L. A., & Verhalen, L. M. (2002). Four near-isogenic lines of cotton with different genes for bacterial blight resistance. //Phytopathology//, //92// (12), 1323-1328.‏
+  - Essenberg, M., Bayles, M. B., Samad, R. A., Hall, J. A., Brinkerhoff, L. A., & Verhalen, L. M. (2002). Four near-isogenic lines of cotton with different genes for bacterial blight resistance. //Phytopathology//, //92//  (12), 1323-1328.‏
-  - Swarup, S., Yang, Y., Kingsley, M. T., & Gabriel, D. W. (1992). An Xanthomonas citri pathogenicity gene, pthA, pleiotropically encodes gratuitous avirulence on nonhosts. //Mol Plant Microbe Interact//, //5// (3), 204-213.‏
+  - Swarup, S., Yang, Y., Kingsley, M. T., & Gabriel, D. W. (1992). An Xanthomonas citri pathogenicity gene, pthA, pleiotropically encodes gratuitous avirulence on nonhosts. //Mol Plant Microbe Interact//, //5//  (3), 204-213.‏
 fagales
@@ Line 586: / Line 1996: @@
   - Potnis, N., Minsavage, G., Smith, J. K., Hurlbert, J. C., Norman, D., Rodrigues, R., … & Jones, J. B. (2012). Avirulence proteins AvrBs7 from Xanthomonas gardneri and AvrBs1. 1 from Xanthomonas euvesicatoria contribute to a novel gene-for-gene interaction in pepper. Molecular plant-microbe interactions, 25(3) : 307-320.
   - Jones, J. B., Minsavage, G. V., Roberts, P. D., Johnson, R. R., Kousik, C. S., Subramanian, S., & Stall, R. E. (2002). A non-hypersensitive resistance in pepper to the bacterial spot pathogen is associated with two recessive genes. Phytopathology, 92(3): 273-277.
-  - Vallejos, C. E., Jones, V., Stall, R. E., Jones, J. B., Minsavage, G. V., Schultz, D. C., … & Mazourek, M. (2010). Characterization of two recessive genes controlling resistance to all races of bacterial spot in peppers. //Theoretical and applied genetics//, //121// (1): 37-46.
+  - Vallejos, C. E., Jones, V., Stall, R. E., Jones, J. B., Minsavage, G. V., Schultz, D. C., … & Mazourek, M. (2010). Characterization of two recessive genes controlling resistance to all races of bacterial spot in peppers. //Theoretical and applied genetics//, //121//  (1): 37-46.
 populus
@@ Line 644: / Line 2054: @@
 wheat
-  - Tyrka, M., & Chelkowski, J. (2004). Enhancing the resistance of triticale by using genes from wheat and rye. //Journal of Applied Genetics//, //45// (3), 283-296.
+  - Tyrka, M., & Chelkowski, J. (2004). Enhancing the resistance of triticale by using genes from wheat and rye. //Journal of Applied Genetics//, //45//  (3), 283-296.
-  - Duveiller, E., van Ginkel, M., & Thijssen, M. (1992). Genetic analysis of resistance to bacterial leaf streak caused by Xanthomonas campestris pv. undulosa in bread wheat. //Euphytica//, //66// (1-2), 35-43.
+  - Duveiller, E., van Ginkel, M., & Thijssen, M. (1992). Genetic analysis of resistance to bacterial leaf streak caused by Xanthomonas campestris pv. undulosa in bread wheat. //Euphytica//, //66//  (1-2), 35-43.
-  - Adhikari, T. B., Gurung, S., Hansen, J. M., Jackson, E. W., & Bonman, J. M. (2012). Association mapping of quantitative trait loci in spring wheat landraces conferring resistance to bacterial leaf streak and spot blotch. //The Plant Genome//, //5// (1), 1-16.
+  - Adhikari, T. B., Gurung, S., Hansen, J. M., Jackson, E. W., & Bonman, J. M. (2012). Association mapping of quantitative trait loci in spring wheat landraces conferring resistance to bacterial leaf streak and spot blotch. //The Plant Genome//, //5//  (1), 1-16.
 rice

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