Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, Njau P, et al. The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol. 2011;49:465–81.
Article
CAS
PubMed
Google Scholar
Wellings CR. Global status of strip rust: a review of historical and current threats. Euphytica. 2011;179:129–41.
Article
Google Scholar
Avelino J, Christancho M, Georgiou S, Imbach P, Aguilar L, Bornemann G, et al. The coffee rust crises in Columbia and Central America (2008–2013): impacts, plausible causes and proposed solutions. Food Sec. 2015;7:303–21.
Article
Google Scholar
Kolmer JA, Ordonez ME, Groth JV. The rust fungi. In: Encyclopedia of Life Sciences (ELS). Chichester: John Wiley and Sons, Ltd; 2009. doi:10.1002/9780470015902.a0021264.
Google Scholar
Li X, Esker PD, Pan Z, Dias AP, Xue L, Yang XB. The uniqueness of the soybean rust pathosystem: an improved understanding of the risk in different regions of the world. Plant Dis. 2010;94:796–806.
Article
Google Scholar
Pinon J, Frey P. Interactions between poplar clones and Melampsora populations and their implications for breeding durable resistance. In: Pei MH, McCracken AR, editors. Rust Diseases of Willow and Poplar. Wallingford: CAB International; 2005. p. 139–54.
Carnegie AJ, Cooper K. Emergency response to the incursion of an exotic myrtaceous rust in Australia. Australas Plant Pathol. 2011;40:346–59.
Article
Google Scholar
Flor HH. Host-parasite interaction in flax rust–its genetics and other implications. Phytopathol. 1955;45:680–5.
Google Scholar
Hammond-Kosack KE, Jones JDG. Resistance gene-dependent plant defense responses. Plant Cell. 1996;8:1773–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernoux M, Ellis JG, Dodds PN. New insights in plant immunity signalling activation. Curr Opin Plant Biol. 2011;14:512–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takken FL, Goverse A. How to build a pathogen detector: structural basis of NB-LRR function. Curr Opin Plant Biol. 2012;15:375–84.
Article
CAS
PubMed
Google Scholar
Hogenhout SA, Van der Hoorn RAL, Terauchi R, Kamoun S. Emerging concepts in effector biology of plant-associated organisms. Mol Plant Microbe Interact. 2009;22:115–22.
Article
CAS
PubMed
Google Scholar
Koeck M, Hardham AR, Dodds PN. The role of effectors of biotrophic and hemibiotrophic fungi in infection. Cell Microbiol. 2011;13:1849–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ökmen B, Doehlemann G. Inside plant: biotrophic strategies to modulate host immunity and metabolism. Curr Opin Plant Biol. 2014;20:19–25.
Article
PubMed
CAS
Google Scholar
Win J, Chaparro-Garcia A, Belhaj K, Saunders DG, Yoshida K, Dong S, et al. Effector biology of plant-associated organisms: concepts and perspectives. Cold Spring Harb Symp Quant Biol. 2012;77:235–47.
Article
CAS
PubMed
Google Scholar
Barrett LG, Thrall PH, Dodds PN, van der Merwe M, Linde CC, Lawrence GJ, et al. Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini. Mol Biol Evol. 2009;26:2499–513.
Article
CAS
PubMed
PubMed Central
Google Scholar
Catanzariti A-M, Dodds PN, Lawrence GJ, Ayliffe MA, Ellis JG. Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors. Plant Cell. 2006;18:243–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dodds PN, Lawrence GJ, Catanzariti A-M, Ayliffe MA, Ellis JG. The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells. Plant Cell. 2004;16:755–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garnica DP, Nemri A, Upadhyaya NM, Rathjen JP, Dodds PN. The ins and outs of rust haustoria. PLoS Pathog. 2014;10:e1004329.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mendgen K, Hahn M. Plant infection and the establishment of fungal biotrophy. Trends Plant Sci. 2002;7:352–6.
Article
CAS
PubMed
Google Scholar
Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, et al. Insights from the genome of the biotrohpic fungal plant pathogen Ustilago maydis. Nature. 2006;444:97–101.
Article
PubMed
CAS
Google Scholar
Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw A, Couloux A, et al. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun. 2011;2:202.
Article
PubMed
PubMed Central
CAS
Google Scholar
Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, et al. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 2011;7:e1002230.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, et al. The Fusarium graminearum genome reveals a link between localised polymorphism and pathogen specialization. Science. 2007;317:1400–2.
Article
CAS
PubMed
Google Scholar
Goodwin SB, M’barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, et al. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet. 2011;7:e1002070.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, et al. The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet. 2012;8:e1003088.
Article
PubMed
PubMed Central
CAS
Google Scholar
Duplessis S, Cuomo CA, Lin Y-C, Aerts A, Tisserant E, Veneault-Fourrey C, et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A. 2011;108:9166–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nemri A, Saunders DGO, Anderson C, Upadhyaya NM, Win J, Lawrence GJ, et al. The genome sequence and effector complement of the flax rust pathogen Melampsora lini. Front Plant Sci. 2014;5:98.
Article
PubMed
PubMed Central
Google Scholar
Zheng W, Huang L, Huang J, Wang X, Chen X, Zhao J, et al. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. Nat Commun. 2013;4:2673.
PubMed
PubMed Central
Google Scholar
Anderson CL, Kubisiak TL, Nelson CD, Smith JA, Davis JM. Genome size variation in the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry. Mycologia. 2010;102:1295–302.
Article
PubMed
Google Scholar
Ramos AP, Tavares S, Tavares D, do Céu Silva M, Loureiro J, Talhinhas P. Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported–2489 Mbp. Mol Plant Pathol. 2015;16:1006–10.
Article
CAS
PubMed
Google Scholar
Tavares S, Ramos AP, Pires AS, Azinheira HG, Caldeirinha P, Link T, et al. Genome size analyses of Pucciniales reveal the largest fungal genomes. Front Plant Sci. 2014;5:422.
Article
PubMed
PubMed Central
Google Scholar
Upadyaya NM, Garnica DP, Karaoglu H, Nemri A, Sperschneider J, Xu B, et al. Comparative genomics of Australian stem rust isolates reveals extensive polymorphism in candidate effector genes. Front Plant Sci. 2015;5:543.
Google Scholar
Cantu D, Govindarajulu M, Kozik A, Wang M, Chen X, Kojima KK, et al. Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. PLoS One. 2011;6:e24230.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM, Escobar C, et al. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. Front Plant Sci. 2014;5:594.
Article
PubMed
PubMed Central
Google Scholar
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6:e19379.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3:e3376.
Article
PubMed
PubMed Central
CAS
Google Scholar
Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, et al. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of the chickpea reference genome assembly. BMC Genomics. 2014;15:708.
Article
PubMed
PubMed Central
CAS
Google Scholar
Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens H-J, Crooijmans RPMA, et al. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 2009;19:510–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
International Cassava Genetic Map Consortium (ICGMC). High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations. G3 (Bethesda). 2015;5:133–44.
Google Scholar
Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature. 2013;496:91–5.
Article
CAS
PubMed
Google Scholar
Reddy UK, Nimmakayala P, Levi A, Abburi VL, Saminathan T, Tomason YR, et al. High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon. G3 (Bethesda). 2014;4:2219–30.
Article
Google Scholar
Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, et al. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet. 2013;126:2699–716.
Article
CAS
PubMed
Google Scholar
Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G, Sweetingham MW, et al. Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus augustifolius L. PLoS One. 2013;8:e64799.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lendenmann MH, Croll D, Palma-Guerrero J, Stewart EL, McDonald BA. QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici. Heredity. 2016;116:384–94.
Article
CAS
PubMed
Google Scholar
Lendenmann MH, Croll D, Stewart EL, McDonald BA. Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici. G3 (Bethesda). 2014;4:2519–33.
Article
Google Scholar
Leboldus JM, Kinzer K, Richards J, Ya Z, Yan C, Friesen TL, et al. Genotyping-by-sequencing of the plant-pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology. Mol Plant Pathol. 2015;16:623–32.
Article
CAS
PubMed
Google Scholar
Lawrence GJ, Mayo GME, Shepherd KW. Interactions between genes controlling pathogenicity in the flax rust fungus. Phytopathol. 1981;71:12–9.
Article
Google Scholar
Jones DA. Genetic properties of inhibitor genes in flax rust that alter avirulence to virulence on flax. Phytopathol. 1988;78:342–4.
Article
Google Scholar
M. lini genome assembly. http://webapollo.bioinformatics.csiro.au:8080/melampsora_lini/. Accessed 24 Dec 2015.
Flor HH. Inheritance of smooth-spore-wall and pathogenicity in Melampsora lini. Phytopathol. 1965;55:724–7.
Google Scholar
Dodds P, Thrall P. Recognition events and host-pathogen co-evolution in gene-for-gene resistance to flax rust. Funct Plant Biol. 2009;36:395–408.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.
Article
CAS
PubMed
Google Scholar
Hiller K, Grote A, Scheer M, Münch R, Jahn D. PrediSi: prediction of signal peptides and their cleavage positions. Nulc Acids Res. 2004;32:W375–9.
Article
CAS
Google Scholar
Boehm EWA, Bushnell WR. An ultrastructural pachytene karyotype for Melampsora lini. Phytopathol. 1992;82:1212–8.
Article
Google Scholar
Lawrence GJ. Multiple mating type specificities in the flax rust Melampsora lini. Science. 1980;209:501–3.
Article
CAS
PubMed
Google Scholar
Gale LR, Bryant JD, Calvo S, Giese H, Katan T, O’Donnell K, et al. Chromosome complement of the fungal plant pathogen Fusarium graminearum based on genetic and physical mapping and cytological observations. Genetics. 2005;171:985–1001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ellwood SR, Liu Z, Syme RA, Lai Z, Hane JK, Keiper F, et al. A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biol. 2010;11:R109.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev Genet. 2013;14:157–67.
Article
CAS
PubMed
Google Scholar
Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012;13:36–46.
CAS
Google Scholar
Fierst JL. Using linkage maps to correct and scaffold de novo assemblies: methods, challenges, and computational tools. Front Genet. 2015;6:220.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lewin HA, Larkin DM, Pontius J, O’Brien SJ. Every genome sequence needs a good map. Genome Res. 2009;19:1925–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front Genet. 2014;5:208.
Article
PubMed
PubMed Central
CAS
Google Scholar
Berchowitz LE, Copenhaver GP. Genetic interference: Don’t stand so close to me. Curr Genomics. 2010;11:91–102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsai CJ, Mets DG, Albrecht MR, Nix P, Chan A, Meyer BJ. Meiotic crossover number and distribution are regulated by a dosage compensation protein that resembles a condensin subunit. Genes Dev. 2008;22:194–211.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pardo-Manuel de Villena F, Sapienza C. Recombination is proportional to the number of chromosome arms in mammals. Mamm Genome. 2001;12:318–22.
Article
CAS
PubMed
Google Scholar
Segura J, Ferretti L, Ramos-Onsins S, Capilla L, Farré M, Reis F, et al. Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference. Proc R Soc B. 2013;280:20131945.
Article
PubMed
PubMed Central
Google Scholar
Salomé PA, Bomblies K, Fitz J, Laitinen RAE, Warthmann N, Yant L, et al. The recombination landscape in Arabidopsis thaliana F2 populations. Heredity. 2012;108:447–55.
Article
PubMed
Google Scholar
Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature. 2008;454:479–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kubisiak TL, Anderson CL, Amerson HV, Smith JA, Davis JM, Nelson CD. A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme. Fungal Genet Biol. 2011;48:266–74.
Article
CAS
PubMed
Google Scholar
Mézard C, Jahns MT, Grelon M. Where to cross? New insights into the location of meiotic crossovers. Trends Genet. 2015;31:393–401.
Article
PubMed
CAS
Google Scholar
Ma J, Wing RA, Bennetzen JL, Jackson SA. Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 2007;23:134–9.
Article
CAS
PubMed
Google Scholar
Talbert PB, Henikoff S. Centromeres convert but don’t cross. PLoS Biol. 2010;8:e1000326.
Article
PubMed
PubMed Central
CAS
Google Scholar
de Massy B. Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. Annu Rev Genet. 2013;47:563–99.
Article
PubMed
CAS
Google Scholar
Henderson IR. Control of meiotic recombination frequency in plant genomes. Curr Opin Plant Biol. 2012;15:556–61.
Article
CAS
PubMed
Google Scholar
Lawrence GJ, Dodds PN, Ellis JG. Rust of flax and linseed caused by Melampsora lini. Mol Plant Pathol. 2007;8:349–64.
Article
PubMed
Google Scholar
Stuckenbrock EH, Croll D. The evolving fungal genome. Fungal Biol Rev. 2014;28:1–12.
Article
Google Scholar
Zolan ME. Chromosome-length polymorphism in fungi. Microbiol Rev. 1995;59:686–98.
CAS
PubMed
PubMed Central
Google Scholar
Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, et al. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact. 2012;25:1350–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anderson PA, Lawrence GJ, Morrish BC, Ayliffe MA, Finnegan EJ, Ellis JG. Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. Plant Cell. 1997;9:641–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ellis JG, Lawrence GJ, Luck JE, Dodds PN. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell. 1999;11:495–506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawrence GJ, Anderson PA, Dodds PN, Ellis JG. Relationships between rust resistance genes at the M locus in flax. Mol Plant Pathol. 2010;11:19–32.
Article
CAS
PubMed
Google Scholar
McLennan AG. The nudix hydrolase superfamily. Cell Mol Life Sci. 2006;63:123–43.
Article
CAS
PubMed
Google Scholar
Dong S, Yin W, Kong G, Yang X, Qutob D, Chen Q, et al. Phytophthora sojae avirulence effector Avr3b is a secreted NADH and ADP-ribose pyrophosphorylase that modulates plant immunity. PLoS Pathog. 2011;7:e1002353.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bhadauria V, Banniza S, Vandenberg A, Selvaraj G, Wei Y. Overexpression of a novel biotrophy-specific Colletotrichum truncatum effector, CtNUDIX, in hemibiotrophic fungal phytopathogens causes incompatibility with their host plants. Eukaryot Cell. 2013;12:2–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura N, Murata Y, Mukaihara T. Isolation of Ralstonia solanacearum hrpB constitutive mutants and secretion analysis of hrpB-regulated gene products that share homology with known type III effectors and enzymes. Microbiology. 2005;151:2873–84.
Article
CAS
PubMed
Google Scholar
Bartsch M, Gobbato E, Bednarek P, Debey S, Schultze JL, Bautor J, et al. Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the nudix hydrolase NUDT7. Plant Cell. 2006;18:1038–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Raffaele S, Win J, Cano LM, Kamoun S. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics. 2010;11:637.
Article
PubMed
PubMed Central
CAS
Google Scholar
Farman ML. Telomeres in the rice blast fungus Magnaporthe oryzae: the world of the end as we know it. FEMS Microbiol Lett. 2007;273:125–32.
Article
CAS
PubMed
Google Scholar
Huang J, Si W, Deng Q, Li P, Yang S. Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet. 2014;15:45.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gout L, Kuhn ML, Vincenot L, Bernard-Samain S, Cattolico L, Barbetti M, et al. Genome structure impacts molecular evolution at the AvrLm1 avirulence locus of the plant pathogen Leptosphaeria maculans. Environ Microbiol. 2007;9:2978–92.
Article
CAS
PubMed
Google Scholar
Ravensdale M, Nemri A, Thrall PH, Ellis JG, Dodds PN. Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease. Mol Plant Pathol. 2011;12:93–102.
Article
CAS
PubMed
Google Scholar
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, et al. Classification of intrinsically disordered regions and proteins. Chem Rev. 2014;114:6589–631.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wright PE, Dyson HJ. Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol. 2015;16:18–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun F, Kale SD, Azurmendi HF, Li D, Tyler BM, Capelluto DG. Structural basis for interactions of the Phytophthora sojae RxLR effector Avh5 with phosphatidylinositol 3-phosphate and for host cell entry. Mol Plant Microbe Interact. 2013;26:330–44.
Article
CAS
PubMed
Google Scholar
Yaeno T, Li H, Chaparro-Garcia A, Schornack S, Koshiba S, Watanabe S, et al. Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity. Proc Natl Acad Sci U S A. 2011;108:14682–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pretsch K, Kemen A, Kemen E, Geiger M, Mendgen K, Voegele R. The rust transferred proteins–a new family of effector proteins exhibiting protease inhibitor function. Mol Plant Pathol. 2013;14:96–107.
Article
CAS
PubMed
Google Scholar
Marín M, Uversky VN, Ott T. Intrinsic disorder in pathogen effectors: protein flexibility as an evolutionary hallmark in a molecular arms race. Plant Cell. 2013;25:3153–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Barrett LG, Thrall PH, Burdon JJ, Nicotra AB, Linde CC. Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini. Mol Ecol. 2008;17:3401–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pernaci M, De Mita S, Andrieux A, Pétrowski J, Halkett F, Duplessis S, et al. Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Front Plant Sci. 2014;5:454.
Article
PubMed
PubMed Central
Google Scholar
Zambino PJ, Kubelik AR, Szabo LJ. Gene action and linkage of avirulence genes to DNA markers in the rust fungus Puccinia graminis. Phytopathol. 2000;90:819–26.
Article
CAS
Google Scholar
Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In: Orgogozo V, Rockman MV, editors. Molecular Methods for Evolutionary Genetics, Methods in Molecular Biology, vol. 772. New York: Humana Press; 2011. p. 157–78.
Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda). 2011;1:171–82.
Article
CAS
Google Scholar
MAPcheck code repository. https://bitbucket.org/cameronjack/mapcheck. Accessed 1 Dec 2015.
Wu Y, Bhat PR, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 2008;4:e1000212.
Article
PubMed
PubMed Central
CAS
Google Scholar
Solovyev V, Kosarev P, Seledsov I, Vorobyev D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006;7 Suppl 1:10.1–10.12.
Article
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.
Article
PubMed
PubMed Central
Google Scholar
Kozlowski LP, Bujnicki JM. MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinf. 2012;13:111.
Article
Google Scholar
Earley KW, Haag JR, Pontes O, Opper K, Juehne T, Song K, et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 2006;45:616–29.
Article
CAS
PubMed
Google Scholar