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A Adaptation, 141 Aeciospores, 180 Agrobacterium-Mediated Index A Biosynthesis gene clusters, 107 Adaptation, 141 Biotechnology applications, 93 Aeciospores, 180 Biotrophic, 125, 131, 154 Agrobacterium-mediated transformation, 185 Biotrophy, 74 Alternaria, 125 Biotrophy-associated secreted (BAS) proteins, 155 Alternate host, 180 Biotrophy-interfacial complexes (BICs), 142, 155 Alternative splicing, 148 Black Sigatoka, 123 AMP domains, 55 Botrytis, 162 Amplified fragment length polymorphism (AFLP), 7, Broad Institute, The, 28, 142, 146, 188 185, 186 Brown leaf spot, 15 Anamorph, 2, 141 Brown spot of rice, 45 Ancestral state, 92 Anthracnose, 69, 77 Antifungal, 84 C Apoplastically, 155 Ca2+/calcineurin, 153 Appressoria, 70, 88, 89, 91, 125, 132, 147 Calcium signaling, 153 Appressorium, 71, 142, 151, 154, 163, 181 Candidate effector proteins, 58 Arabidopsis, 77 Candidate secreted effector proteins (CSEPs), 171 Ascomycete core genes, 169 Carbohydrate binding, 87 Ascospore development, 111 Carbohydrate-active enzymes (CAZymes), 82, 187 Ascospore, 103, 104, 125, 163 cDNA, 146 Association study, 145 Cell wall associated genes, 148 AT-rich sequences, 78 Cell wall biosynthesis, 154 Autophagy, 142, 151, 153 Cell wall degrading enzymes (CWDE), 20, 71, 111, 130, Auxin, 84 131, 132, 164 Avirulence, 185, 186 CFEM, 147 Avirulence genes, 141, 144, 189, 191 Chasmothecium, 164 Avr genes, 144 Chitinases, 132 Avr4, 131, 132 Chloroplast localization of ToxA, 12 Axenic culture, 181 Chloroplasts, 14 Chromosome structure, 134 Cladosporium fulvum, 131 B Clusters, 80, 84 BAC clones, 127 Cochliobolus spp., 41, 125 Banana, 123 Cochliobolus carbonum, 43 Barberries, 177 Cochliobolus genomes, 47 Barberry eradication, 180 Cochliobolus heterostrophus, 41 BBAC libraries, 166 Cochliobolus miyabeanus, 45 Berberine bridge-containing flavoproteins (BBEs), 20 Cochliobolus sativus, 43 Biochemical pathways, 153 Cochliobolus victoriae, 43 Bioenergy crops, 70 Coevolutionary, 92, 172 Biofuels, 94 Colletotrichum Comparative Genomics, 78 R. A. Dean et al. (eds.), Genomics of Plant-Associated Fungi: Monocot Pathogens, 197 DOI: 10.1007/978-3-662-44053-7, Ó Springer-Verlag Berlin Heidelberg 2014 198 Index Colonization, 75 Fusarium graminearum, 103, 104 Comparative analyses, 50, 133 Fusarium head blight (FHB), 104 Comparative genome, 80 Fusarium pseudograminearum, 104 Comparative genome analyses, 90, 141 Comparative genome studies, 144 Comparative genomics, 156 G Conditionally dispensable chromosomes, 145 G protein coupled receptors (GPCRs), 60, 113 Conidia, 1 G proteins, 111 Conidiation, 147 Gaeumannomyces graminis var. tritici, 144 Conidiospore, 142, 163 Gene duplication, 78 Control, 182 Gene expression, 147, 148 Convergent evolution, 170 Gene families, 82 Copy number variation (CNV), 24 Gene silencing, 29 Cross-species recognition, 132 Genetic analyses, 166 Curvularia lunata, 45 Genetic diversity, 7, 29 Cutinases, 88 Genetic map, 126, 189 Cyclic AMP (cAMP), 70, 88, 147, 153, 156 Genetic studies, 184 Cytochromes P450 (CYPs), 58 Genetic variability, 8, 123 Cytological studies, 90 Genome architecture, 136 Genome comparison studies, 145 Genome rearrangement and expansion, 29 D Genome rearrangements, 79 Defense-related pathways, 15 Genome sequence, 77 Diagnosis, 92 Genome size, 78, 146 Diagnostic assay, 191 Genome structure, 127, 166, 186 Disease cycle, 125 Global gene, 154 Dispensable chromosomes, 128 Glomerellaceae, 71 Dispensome, 130, 131, 133 Glyoxylate cycle, 151 Divergence, 92 Green fluorescent protein (GFP), 12 Diversification, 187 GUY11, 143 Diversifying selection, 144, 171 Dominant host sensitivity (susceptibility) genes, 8 DON biosynthesis gene Tri5, 114 H Dothideomycetes, 2, 124 Hairpin RNAs, 150 Duplications, 131, 145 hAT (hobo-Activator-Tam3) superfamily, 23 Haustoria, 89, 91, 172, 187, 188, 191 Haustorium, 164 E HC-toxin, 43, 50 Ear rot and stalk rot of maize, 103, 105 Hemibiotroph, 56, 58, 59 Economic importance, 177 Hemibiotrophic, 73, 135 Ecp2, 131, 132 Hemibiotrophic lifestyle, 91 Effector, 59, 62, 80, 82, 85-90, 116, 131, 132, 136, 144, Heterothallic, 45, 46, 111, 126 154, 155, 167, 170, 173, 187, 189, 190, 191 Heterotrimeric G protein, 59 Endophytic, 75 HGT between organisms, 24 Endoplasmic reticulum (ER), 155 Histidine kinase sensors, 59 Epidemic, 141, 142 Histone deacetylase, 43 Epiphytes, 76 Histone H3-like gene, 23 Evolution, 123 HMG box, 82 Expressed sequence tags (ESTs), 88 Homing endonuclease genes, 17, 18 Extremely large size of the Ptr mitochondrial genome, 18 Homologous recombination, 126 Homothallic, 45, 46, 82, 111 Horizontal gene transfer (HGT), 19, 55 F Horizontal transfer, 81, 130 Formae speciales, 163, 179, 164 Host association, 92 Forward genetics, 108 Host range, 181 Fungicides, 182 Host response in susceptibility, 13 Fusarium graminearum species complex (FGSC), 104 Host targets, 155 Fusarium graminearum transcription factor phenotype Host-induced gene silencing system (HIGS), 165, 189 database (FgTFPD), 114 Host-selective toxins (HSTs), 4, 11, 12, 19, 41 Index 199 Hydrophobins, 169 Microsatellite, 126 Hypersensitive, 132 Microsclerotia, 76 Microsynteny, 134 Miniature inverted-repeat transposable elements I (MITES), 22 Idiomorphs, 81 Minichromosomes, 81 in planta EST library, 27 Mitochondria, 16, 17 in planta transcripts, 27 Mitochondrial genomes, 17, 18 Infection hyphae, 89 mlo genes, 161 Infection process, 10, 181 Molecular detection approaches, 115 Inheritance, 185 Molecular diagnostics, 190 Internal transcribed spacer (ITS), 2 Molecular markers, 190 Invasion, 154 Molecular phylogenetic approaches, 92 Invasive, 151 Monophyletic clades, 71 Inverse gene-for-gene interactions, 15 Mutants, 150 Inversions, 134, 135 Mycosphaerella graminicola, 18 Iron, 50, 55, 56 Mycosphaerellaceae, 124 Isochores, 167 Mycotoxins, 103, 113, 115, 133 ITS sequence, 71 N J NB-LRR-type resistance protein (LOV1), 43 Joint Genome Institute (JGI), 28, 46, 127 NBS-LRR, 144 Necrosis- and ethylene- inducing peptide (NEP), 85 Necrotrophic, 73, 126, 142 K Necrotrophic effector molecules, 59 Karyotypic analysis, 186 Necrotrophic pathogen, 10 Kinase, 148, 150 Necrotrophs, 49, 56 Kyoto Encyclopedia of Genes and Genomes (KEGG), Net blotch of barley, 15 152 New fungicides, 133 New races of Ptr, 7 Nitrate assimilation, 187 L Nitrogen limitation (NL), 147 Laser-capture microscopy (LCM), 87 Non-ribosomal peptide synthetases (NRPS), 21, 45, 49, Life cycle, 125, 128, 142, 150, 163, 180, 191 50, 55, 84, 144 Lifestyle, 71, 73, 76, 90 Northern Corn Leaf Spot, 43 Light regulation, 61 O M Obligate biotrophic, 162 Macroconidia, 103, 104 Optical genetic map, 16 Macrosynteny, 134 Oxidative stress, 55, 57, 61, 62, 150 Major genes, 132 Oxidative stress related genes, 56 Management, 76, 91, 124 MAP kinase, 59, 70 MAPK cascade, 111 P MAT genes, 46 p450s, 20 MAT1-1, 46, 111 Panicle blast, 141 MAT1-2, 46, 111 Papilla, 164 Mating, 126 Particle bombardment, 185 Mating type, 81, 165 Pathogen-associated molecular pattern (PAMP) elicitors, Mating type genes, 135 76 Mating type locus (MAT), 8, 45 Pathogenesis-related (PR) proteins, 132 Melanin, 84, 88, 142, 151 Pectin, 83 Melanin biosynthesis, 50 Penetration, 88, 151, 154 Mesosynteny, 48, 134, 135 Penetration peg, 181 Metabolic pathways, 152, 187 Perithecia, 111 Metabolomics, 152 Pheromone, 111 Microarray, 87, 110, 146, 155, 148, 187 Pheromone receptor, 111 200 Index Photosystem II, 14 Resistance, 124, 132, 133, 141, 156, 178, 182, 183 Phylogenetic, 93, 178 Resistance (R) genes, 123, 161 Phylogenetic analysis, 136, 192 Resistant cultivars, 91 Phylogenetic studies, 142 Restriction enzyme-mediated integration (REMI), 108 Phylogenetic tree, 77 Retrotransposon, 80, 128, 131, 167 Phylogenomic analysis, 92 Reverse genetic, 108, 151 Physiologic specialization, 5 RFLP markers, 186 Physiological races, 70 RGD (Arg-Gly-Asp), 11 Phytoalexins, 70 RIA, 55 Phytotoxins, 84 RNA interference (RNAi), 150, 165, 189 Plant host-pathogen interactions, 10 RNA silencing, 185 Plastic genome, 23 RNA-seq, 110, 141 Pleosporaceae, 2 Rot, 69, 77 Pleosporales, 2 Rpg1, 184, 189 Polyethylene glycol (PEG) transformation, 109 rpg4, 184 Polyketide synthases (PKS), 21, 49, 84, 144 Rpg5, 184 Polyphagous, 164 RXLR-like motif, 188 Polyploidy, 131 Polysaccharide degrading enzymes, 169 Population diversity, 111 S Population genetics, 190 Saprotrophic, 76 Postgenomic, 90 Scaffolds, 127 Primary metabolism, 169 Sclerotinia, 162 Protein families, 186 Secondary metabolism, 62, 154 Protein secretion systems, 190 Secondary metabolism (SM) enzymes, 82 Proteomics, 110, 141, 152, 153 Secondary metabolism genes, 50, 55, 83 PSI, 14 Secondary metabolite, 50, 133, 169 PSII, 14 Secondary metabolite (SM) effectors, 76 Pt-1C-BFP, 15 Secreted genes, 81, 147 Ptr ToxA, 5, 9 Secreted proteases, 85 Ptr ToxB, 5 Secretion, 155 Ptr ToxC, 5 Secretome, 85 Pycnidiospores, 125 Septoria tritici blotch (STB), 123 Pyrenophora teres, 15 Sexual cycle, 164 Pyrenophora bromi, 13, 15 Short interspersed nuclear elements (SINEs), 22 Pyrenophora tritici-repentis (Ptr), 1 Siderophore, 55, 84 Pyrenophora, 125 Siderophore biosynthesis, 50 Signal transduction, 147 Signaling pathways, 70, 92 Q Signaling, 71 Quinate, 152 Silencing, 78 Single nucleotide polymorphism (SNP), 25, 144, 146 Small interfering RNAs (siRNAs), 150 R Small secreted proteins (SSPs), 58, 62, 80, 85-87, 88, Race 1, 15 144, 154, 188 Races of Ptr, 5 Smooth bromegrass, 15 Random amplified polymorphic DNA (RAPD), 7, 185 Somatic fusion, 135 Random gene insertion, 78 Southern Corn Leaf Blight (SCLB), 41 Random insertions, 149 Speciation, 131 rDNA, 178 Species concepts, 92 Reactive oxygen species (ROS), 14, 150, 152 Species-specific,
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