REFERENCES
- Adler, D., Nenadic, O., & Zucchini, W. (2017). RGL: A R-library for
3D visualization with OpenGL.
- Andolfo, G., Di Donato, A., Chiaiese, P., De Natale, A., Pollio, A.,
Jones, J. D. G., . . . Ercolano, M. R. (2019). Alien Domains Shaped
the Modular Structure of Plant NLR Proteins. Genome Biology and
Evolution, 11 (12), 3466-3477. doi:10.1093/gbe/evz248
- Baggs, E., Dagdas, G., & Krasileva, K. V. (2017). NLR diversity,
helpers and integrated domains: making sense of the NLR IDentity.Current Opinion in Plant Biology, 38 , 59-67.
doi:10.1016/j.pbi.2017.04.012
- Berardini, T. Z., Reiser, L., Li, D., Mezheritsky, Y., Muller, R.,
Strait, E., & Huala, E. (2015). The Arabidopsis information resource:
Making and mining the ”gold standard” annotated reference plant
genome. Genesis, 53 (8), 474-485. doi:10.1002/dvg.22877
- Bergelson, J., Kreitman, M., Stahl, E. A., & Tian, D. (2001).
Evolutionary Dynamics of Plant Genes. Science, 292 (5525),
2281-2285. doi:10.1126/science.1061337 %J Science
- Bever, J. D., Mangan, S. A., & Alexander, H. M. (2015). Maintenance
of Plant Species Diversity by Pathogens. Annual Review of
Ecology, Evolution, and Systematics, 46 (1), 305-325.
doi:10.1146/annurev-ecolsys-112414-054306
- Bittner-Eddy, P. D., Crute, I. R., Holub, E. B., & Beynon, J. L.
(2000). RPP13 is a simple locus in Arabidopsis thaliana for alleles
that specify downy mildew resistance to different avirulence
determinants in Peronospora parasitica. The Plant Journal,
21 (2), 177-188. doi:10.1046/j.1365-313x.2000.00664.x
- Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a
flexible trimmer for Illumina sequence data. Bioinformatics,
30 (15), 2114-2120. doi:10.1093/bioinformatics/btu170
- Borrelli, G. M., Mazzucotelli, E., Marone, D., Crosatti, C.,
Michelotti, V., Valè, G., & Mastrangelo, A. M. (2018). Regulation and
Evolution of NLR Genes: A Close Interconnection for Plant Immunity.International Journal of Molecular Sciences, 19 (6).
doi:10.3390/ijms19061662
- Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016).
Near-optimal probabilistic RNA-seq quantification. Nature
Biotechnology, 34 (5), 525-527. doi:10.1038/nbt.3519
- Brechenmacher, L., Nguyen, T. H., Zhang, N., Jun, T. H., Xu, D., Mian,
M. A., & Stacey, G. (2015). Identification of Soybean Proteins and
Genes Differentially Regulated in Near Isogenic Lines Differing in
Resistance to Aphid Infestation. Journal of Proteome Research,
14 (10), 4137-4146. doi:10.1021/acs.jproteome.5b00146
- Burghardt, L. T., Guhlin, J., Chun, C. L., Liu, J., Sadowsky, M. J.,
Stupar, R. M., . . . Tiffin, P. (2017). Transcriptomic basis of genome
by genome variation in a legume-rhizobia mutualism. Molecular
Ecology, 26 (21), 6122-6135. doi:10.1111/mec.14285
- Bushnell, W. R. (2002). The role of powdery mildew research in
understanding host-parasite interaction: past, present and future.In The Powdery Mildews , A Comprehensive Treatise (Bélanger, R.
R., Bushnell, W. R., Dik, A. J., and Carver, T. A. W., eds). APS
Press, St. Paul, Minnesota, USA. , 1-12.
- Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J.,
Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and
applications. BMC Bioinformatics, 10 , 421.
doi:10.1186/1471-2105-10-421
- Chandran, D., Inada, N., Hather, G., Kleindt, C. K., & Wildermuth, M.
C. (2010). Laser microdissection of Arabidopsis cells at the powdery
mildew infection site reveals site-specific processes and regulators.Proceedings of the National Academy of Sciences of the United
States of America, 107 (1), 460-465. doi:10.1073/pnas.0912492107
- Chang, S., Puryear, J., & Cairney, J. (1993). A simple and efficient
method for isolating RNA from pine trees. Plant Molecular
Biology Reporter, 11 (2), 113-116.
- Chen, J., Pang, W., Chen, B., Zhang, C., & Piao, Z. (2015).
Transcriptome Analysis of Brassica rapa Near-Isogenic Lines Carrying
Clubroot-Resistant and -Susceptible Alleles in Response to
Plasmodiophora brassicae during Early Infection. Frontiers in
Plant Science, 6 , 1183. doi:10.3389/fpls.2015.01183
- Chisholm, S. T., Coaker, G., Day, B., & Staskawicz, B. J. (2006).
Host-microbe interactions: shaping the evolution of the plant immune
response. Cell, 124 (4), 803-814. doi:10.1016/j.cell.2006.02.008
- Choi, J., Choi, D., Lee, S., Ryu, C. M., & Hwang, I. (2011).
Cytokinins and plant immunity: old foes or new friends? Trends
in Plant Science, 16 (7), 388-394. doi:10.1016/j.tplants.2011.03.003
- Coll, N. S., Epple, P., & Dangl, J. L. (2011). Programmed cell death
in the plant immune system. Cell Death & Differentiation,
18 (8), 1247-1256. doi:10.1038/cdd.2011.37
- Cruz-Miralles, J., Cabedo-Lopez, M., Perez-Hedo, M., Flors, V., &
Jaques, J. A. (2019). Zoophytophagous mites can trigger plant-genotype
specific defensive responses affecting potential prey beyond
predation: the case of Euseius stipulatus and Tetranychus urticae in
citrus. Pest Managment Science, 75 (7), 1962-1970.
doi:10.1002/ps.5309
- Davidson, N. M., Hawkins, A. D. K., & Oshlack, A. (2017).
SuperTranscripts: a data driven reference for analysis and
visualisation of transcriptomes. Genome Biology, 18 (1), 148.
doi:10.1186/s13059-017-1284-1
- Decaestecker, E., Gaba, S., Raeymaekers, J. A., Stoks, R., Van
Kerckhoven, L., Ebert, D., & De Meester, L. (2007). Host-parasite
’Red Queen’ dynamics archived in pond sediment. Nature,
450 (7171), 870-873. doi:10.1038/nature06291
- Dusa, A. (2018). venn: Draw Venn Diagrams. R package, version
1.7.
- Egorov, T. A., & Odintsova, T. I. (2012). Defense peptides of plant
immunity. Russian Journal of Bioorganic Chemistry, 38 (1), 1-9.
doi:10.1134/s1068162012010062
- Fay, J. C., & Wu, C. I. (2000). Hitchhiking under positive Darwinian
selection. Genetics, 155 (3), 1405-1413.
- Fei, Q., Xia, R., & Meyers, B. C. (2013). Phased, Secondary, Small
Interfering RNAs in Posttranscriptional Regulatory Networks. The
Plant Cell, 25 (7), 2400-2415. doi:10.1105/tpc.113.114652
- Fu, Y. B., Peterson, G. W., Horbach, C., Konkin, D. J., Beiles, A., &
Nevo, E. (2019). Elevated mutation and selection in wild emmer wheat
in response to 28 years of global warming. Proceedings of the
National Academy of Sciences (PNAS) USA, 116 (40), 20002-20008.
doi:10.1073/pnas.1909564116
- Gilbert, D. (2013). Gene-omes built from mRNA seq not genome DNA.7th annual arthropod genomics symposium. Notre Dame .
- Gilligan, C. A. (2002). An epidemiological framework for disease
management. In Advances in Botanical Research (Vol. 38, pp.
1-64): Academic Press.
- Gohre, V. (2015). Immune responses: Photosynthetic defence.Nature Plants, 1 , 15079. doi:10.1038/nplants.2015.79
- Gómez, P., & Buckling, A. (2011). Bacteria-Phage Antagonistic
Coevolution in Soil. Science, 332 (6025), 106-109.
doi:10.1126/science.1198767 %J Science
- Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D.
A., Amit, I., . . . Regev, A. (2011). Full-length transcriptome
assembly from RNA-Seq data without a reference genome. Nature
Biotechnology, 29 (7), 644-652. doi:10.1038/nbt.1883
- Greischar, M. A., & Koskella, B. (2007). A synthesis of experimental
work on parasite local adaptation. Ecology Letters, 10 (5),
418-434. doi:10.1111/j.1461-0248.2007.01028.x
- Hahlbrock, K., Scheel, D., Logemann, E., Nürnberger, T., Parniske, M.,
Reinold, S., . . . Schmelzer, E. (1995). Oligopeptide
elicitor-mediated defense gene activation in cultured parsley cells.Proceedings of the National Academy of Sciences of the United
States of America, 92 (10), 4150-4157. doi:10.1073/pnas.92.10.4150
- Hall, S. A., Allen, R. L., Baumber, R. E., Baxter, L. A., Fisher, K.,
Bittner-Eddy, P. D., . . . Beynon, J. L. (2009). Maintenance of
genetic variation in plants and pathogens involves complex networks of
gene-for-gene interactions. Molecular Plant Pathology, 10 (4),
449-457. doi:10.1111/j.1364-3703.2009.00544.x
- Hamilton, W. D. (1980). Sex versus Non-Sex versus Parasite.Oikos, 35 (2), 282-290. doi:10.2307/3544435
- Hockerstedt, L. M., Siren, J. P., & Laine, A. L. (2018). Effect of
spatial connectivity on host resistance in a highly fragmented natural
pathosystem. Journal of Evolutionary Biology, 31 (6), 844-852.
doi:10.1111/jeb.13268
- Hoeksema, J. D., & Forde, S. E. (2008). A meta-analysis of factors
affecting local adaptation between interacting species. The
American Naturalist, 171 (3), 275-290. doi:10.1086/527496
- Hua, L. (2009). Dissection of salicylic acid-mediated defense
signaling networks. Plant Signaling and Behavior, 4 (8),
713-717. doi:10.4161/psb.4.8.9173
- Jacob, F., Vernaldi, S., & Maekawa, T. (2013). Evolution and
Conservation of Plant NLR Functions. Frontiers in Immunology,
4 , 297. doi:10.3389/fimmu.2013.00297
- Jaenike, J. (1978). Host Selection by Mycophagous Drosophila.ECOLOGY, 59 (6), 1286-1288. doi:10.2307/1938245
- Jensen, M. K., Hagedorn, P. H., de Torres-Zabala, M., Grant, M. R.,
Rung, J. H., Collinge, D. B., & Lyngkjaer, M. F. (2008).
Transcriptional regulation by an NAC (NAM-ATAF1,2-CUC2) transcription
factor attenuates ABA signalling for efficient basal defence towards
Blumeria graminis f. sp. hordei in Arabidopsis. The Plant
Journal, 56 (6), 867-880. doi:10.1111/j.1365-313X.2008.03646.x
- Jones, J. D., & Dangl, J. L. (2006). The plant immune system.Nature, 444 (7117), 323-329. doi:10.1038/nature05286
- Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C.,
. . . Hunter, S. (2014). InterProScan 5: genome-scale protein function
classification. Bioinformatics, 30 (9), 1236-1240.
doi:10.1093/bioinformatics/btu031
- Jousimo, Tack, A. J., Ovaskainen, O., Mononen, T., Susi, H.,
Tollenaere, C., & Laine, A. L. (2014a). Ecological and evolutionary
effects of fragmentation on infectious disease dynamics.Science, 344 (6189), 1289-1293. doi:10.1126/science.1253621
- Jousimo, J., Tack, A. J. M., Ovaskainen, O., Mononen, T., Susi, H.,
Tollenaere, C., & Laine, A.-L. (2014b). Ecological and evolutionary
effects of fragmentation on infectious disease dynamics.344 (6189), 1289-1293. doi:10.1126/science.1253621 %J Science
- Kachroo, A., & Kachroo, P. (2009). Fatty Acid-derived signals in
plant defense. Annual Review of Phytopathology, 47 , 153-176.
doi:10.1146/annurev-phyto-080508-081820
- Karim, S., Holmstrom, K. O., Mandal, A., Dahl, P., Hohmann, S.,
Brader, G., . . . Pirhonen, M. (2007). AtPTR3, a wound-induced peptide
transporter needed for defence against virulent bacterial pathogens in
Arabidopsis. Planta, 225 (6), 1431-1445.
doi:10.1007/s00425-006-0451-5
- Klopfenstein, D. V., Zhang, L., Pedersen, B. S., Ramirez, F., Warwick
Vesztrocy, A., Naldi, A., . . . Tang, H. (2018). GOATOOLS: A Python
library for Gene Ontology analyses. Scientific Reports, 8 (1),
10872. doi:10.1038/s41598-018-28948-z
- Koff, R. S. (1992). Infectious diseases of humans: Dynamics and
control. By R.M. Anderson and R.M. May, 757 pp. Oxford: Oxford
University Press, 1991. $95.00. Hepatology, 15 (1), 169-169.
doi:10.1002/hep.1840150131
- Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD:
Analysis of Next Generation Sequencing Data. BMC Bioinformatics,
15 (1), 356. doi:10.1186/s12859-014-0356-4
- Kryazhimskiy, S., & Plotkin, J. B. (2008). The population genetics of
dN/dS. PLoS Genetics, 4 (12), e1000304.
doi:10.1371/journal.pgen.1000304
- Kuniak, E., & Urbanek, H. (2000). The involvement of hydrogen
peroxide in plant responses to stresses. Acta Physiologiae
Plantarum, 22 (2), 95-203.
doi:https://doi.org/10.1007/s11738-000-0076-4
- Kursar, T. A., Dexter, K. G., Lokvam, J., Pennington, R. T.,
Richardson, J. E., Weber, M. G., . . . Coley, P. D. (2009). The
evolution of antiherbivore defenses and their contribution to species
coexistence in the tropical tree genus <em>Inga</em>.Proceedings of the National Academy of Sciences, 106 (43),
18073. doi:10.1073/pnas.0904786106
- Lai, Y., & Eulgem, T. (2018). Transcript-level expression control of
plant NLR genes. Molecular Plant Pathology, 19 (5), 1267-1281.
doi:10.1111/mpp.12607
- Laine, A. L. (2004). Resistance variation within and among host
populations in a plant–pathogen metapopulation: implications for
regional pathogen dynamics. Journal of Ecology, 92 (6),
990-1000. doi:doi:10.1111/j.0022-0477.2004.00925.x
- Laine, A. L. (2005). Spatial scale of local adaptation in a
plant-pathogen metapopulation. Journal of Evolutionary Biology,
18 (4), 930-938. doi:10.1111/j.1420-9101.2005.00933.x
- Laine, A. L. (2006). Evolution of host resistance: looking for
coevolutionary hotspots at small spatial scales. Proceedings of
the Royal Society B: Biological Sciences, 273 (1584), 267-273.
doi:10.1098/rspb.2005.3303
- Laine, A. L. (2007). Pathogen fitness components and genotypes differ
in their sensitivity to nutrient and temperature variation in a wild
plant-pathogen association. Journal of Evolutionary Biology,
20 (6), 2371-2378. doi:10.1111/j.1420-9101.2007.01406.x
- Laine, A. L. (2008). Temperature-mediated patterns of local adaptation
in a natural plant-pathogen metapopulation. Ecology Letters,
11 (4), 327-337. doi:10.1111/j.1461-0248.2007.01146.x
- Laine, A. L., Burdon, J. J., Dodds, P. N., & Thrall, P. H. (2011).
Spatial variation in disease resistance: from molecules to
metapopulations. Journal of Ecology, 99 (1), 96-112.
doi:10.1111/j.1365-2745.2010.01738.x
- Le Roy, J., Huss, B., Creach, A., Hawkins, S., & Neutelings, G.
(2016). Glycosylation Is a Major Regulator of Phenylpropanoid
Availability and Biological Activity in Plants. Frontiers in
Plant Science, 7 , 735. doi:10.3389/fpls.2016.00735
- Leonard, K. J. (1977). Selection pressure and plant pathogens.Annals of the New York Academy of Sciences, 287 (1), 207-222.
doi:10.1111/j.1749-6632.1977.tb34240.x
- Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., & Dewey, C. N.
(2010). RNA-Seq gene expression estimation with read mapping
uncertainty. Bioinformatics, 26 (4), 493-500.
doi:10.1093/bioinformatics/btp692
- Li, G., Xu, X., Bai, G., Carver, B. F., Hunger, R., & Bonman, J. M.
(2016). Identification of Novel Powdery Mildew Resistance Sources in
Wheat. Acess DL, 56 (4), 1817-1830.
doi:10.2135/cropsci2015.09.0551
- Li, H., Dong, Z., Ma, C., Tian, X., Xiang, Z., Xia, Q., . . . Liu, W.
(2019). Discovery of powdery mildew resistance gene candidates from
Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing.PLoS One, 14 (11), e0220089. doi:10.1371/journal.pone.0220089
- Li, M., Zhang, D., Gao, Q., Luo, Y., Zhang, H., Ma, B., . . . Xue, Y.
(2019). Genome structure and evolution of Antirrhinum majus L.Nature Plants, 5 (2), 174-183. doi:10.1038/s41477-018-0349-9
- Liang, P., Liu, S., Xu, F., Jiang, S., Yan, J., He, Q., . . . Miao, W.
(2018). Powdery Mildews Are Characterized by Contracted Carbohydrate
Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic
Lifestyle. Frontiers in Microbiology, 9 , 3160.
doi:10.3389/fmicb.2018.03160
- Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of
fold change and dispersion for RNA-seq data with DESeq2. Genome
Biology, 15 (12), 550. doi:10.1186/s13059-014-0550-8
- McDowell, J. M., & Simon, S. A. (2006). Recent insights into R gene
evolution. Molecular Plant Pathology, 7 (5), 437-448.
doi:10.1111/j.1364-3703.2006.00342.x
- Meunier, E., & Broz, P. (2017). Evolutionary Convergence and
Divergence in NLR Function and Structure. Trends in Immunology,
38 (10), 744-757. doi:10.1016/j.it.2017.04.005
- Meyers, B. C. (2003). Genome-Wide Analysis of NBS-LRR-Encoding Genes
in Arabidopsis. The Plant Cell Online, 15 (4), 809-834.
doi:10.1105/tpc.009308
- Michelmore, R. W., & Meyers, B. C. (1998). Clusters of Resistance
Genes in Plants Evolve by Divergent Selection and a Birth-and-Death
Process. GENOME RESEARCH (8), 1113-1130.
doi:10.1101/gr.8.11.1113
- Miedes, E., Vanholme, R., Boerjan, W., & Molina, A. (2014). The role
of the secondary cell wall in plant resistance to pathogens.Frontiers in Plant Science, 5 , 358. doi:10.3389/fpls.2014.00358
- Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P.,
Bridge, A., . . . Finn, R. D. (2019). InterPro in 2019: improving
coverage, classification and access to protein sequence annotations.Nucleic Acids Research, 47 (D1), D351-D360.
doi:10.1093/nar/gky1100
- Mock, H. P., Keetman, U., Kruse, E., Rank, B., & Grimm, B. (1998).
Defense Responses to Tetrapyrrole-Induced Oxidative Stress in
Transgenic Plants with Reduced Uroporphyrinogen Decarboxylase or
Coproporphyrinogen Oxidase Activity. Plant Physiology, 116 (1),
107. doi:10.1104/pp.116.1.107
- Mohr, T. J., Mammarella, N. D., Hoff, T., Woffenden, B. J., Jelesko,
J. G., & McDowell, J. M. (2010). The Arabidopsis Downy Mildew
Resistance Gene RPP8 Is Induced by Pathogens and Salicylic Acid and Is
Regulated by W Box cis Elements. Molecular Plant-Microbe
Interactions®, 23 (10), 1303-1315. doi:10.1094/MPMI-01-10-0022
- Monteiro, F., & Nishimura, M. T. (2018). Structural, Functional, and
Genomic Diversity of Plant NLR Proteins: An Evolved Resource for
Rational Engineering of Plant Immunity. Annual Review of
Phytopathology, 56 , 243-267. doi:10.1146/annurev-phyto-080417-045817
- Muller, N. A., Kersten, B., Fladung, M., & Schroeder, H. (2019).
RNA-seq of eight different poplar clones reveals conserved
up-regulation of gene expression in response to insect herbivory.BMC Genomics, 20 (1), 673. doi:10.1186/s12864-019-6048-8
- Mundt, C. C. (2002a). Use of multiline cultivars and cultivar mixtures
fo disease management. Annual Review of Phytopathology, 40 (1),
381-410. doi:10.1146/annurev.phyto.40.011402.113723
- Mundt, C. C. (2002b). Use of multiline cultivars and cultivar mixtures
for disease management. 40 (1), 381-410.
doi:10.1146/annurev.phyto.40.011402.113723
- Mundt, C. C. (2014). Durable resistance: a key to sustainable
management of pathogens and pests. Infection, Genetics and
Evolution, 27 , 446-455. doi:10.1016/j.meegid.2014.01.011
- Mur, L. A. J., Simpson, C., Kumari, A., Gupta, A. K., & Gupta, K. J.
(2017). Moving nitrogen to the centre of plant defence against
pathogens. Annals of Botany, 119 (5), 703-709.
doi:10.1093/aob/mcw179
- Niu, L., & Liao, W. (2016). Hydrogen Peroxide Signaling in Plant
Development and Abiotic Responses: Crosstalk with Nitric Oxide and
Calcium. Frontiers in Plant Science, 7 , 230.
doi:10.3389/fpls.2016.00230
- Nürnberger, T., Nennstiel, D., Jabs, T., Sacks, W. R., Hahlbrock, K.,
& Scheel, D. (1994). High affinity binding of a fungal oligopeptide
elicitor to parsley plasma membranes triggers multiple defense
responses. Cell, 78 (3), 449-460.
doi:https://doi.org/10.1016/0092-8674(94)90423-5
- Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P.,
McGlinn, D., . . . Wagner, H. (2018). vegan: Community Ecology
Package. R package, version 2.5-3.
- Perez-Bueno, M. L., Pineda, M., & Baron, M. (2019). Phenotyping Plant
Responses to Biotic Stress by Chlorophyll Fluorescence Imaging.Frontiers in Plant Science, 10 , 1135.
doi:10.3389/fpls.2019.01135
- Phadnis, N., & Malik, H. S. (2014). Speciation via autoimmunity: a
dangerous mix. Cell, 159 (6), 1247-1249.
doi:10.1016/j.cell.2014.11.028
- Pike, S., Gao, F., Kim, M. J., Kim, S. H., Schachtman, D. P., &
Gassmann, W. (2014). Members of the NPF3 transporter subfamily encode
pathogen-inducible nitrate/nitrite transporters in grapevine and
Arabidopsis. Plant and Cell Physiology, 55 (1), 162-170.
doi:10.1093/pcp/pct167
- Plomion, C., Aury, J. M., Amselem, J., Leroy, T., Murat, F.,
Duplessis, S., . . . Salse, J. (2018). Oak genome reveals facets of
long lifespan. Nature Plants, 4 (7), 440-452.
doi:10.1038/s41477-018-0172-3
- Polonio, Á., Pineda, M., Bautista, R., Martínez-Cruz, J., Pérez-Bueno,
M. L., Barón, M., & Pérez-García, A. (2019). RNA-seq analysis and
fluorescence imaging of melon powdery mildew disease reveal an
orchestrated reprogramming of host physiology. Scientific
Reports, 9 (1). doi:10.1038/s41598-019-44443-5
- Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree
2–approximately maximum-likelihood trees for large alignments.PLoS One, 5 (3), e9490. doi:10.1371/journal.pone.0009490
- Pruitt, K. D., Tatusova, T., & Maglott, D. R. (2007). NCBI reference
sequences (RefSeq): a curated non-redundant sequence database of
genomes, transcripts and proteins. Nucleic Acids Research,
35 (Database issue), D61-65. doi:10.1093/nar/gkl842
- Ragonnet-Cronin, M., Hodcroft, E., Hué, S., Fearnhill, E., Delpech,
V., Leigh Brown, A. J., & Lycett, S. (2013). Automated analysis of
phylogenetic clusters. BMC Bioinformatics, 14 (317).
doi:10.1186/1471-2105-14-317
- Rentel, M. C., Leonelli, L., Dahlbeck, D., Zhao, B., & Staskawicz, B.
J. (2008). Recognition of the Hyaloperonospora parasitica effector
ATR13 triggers resistance against oomycete, bacterial, and viral
pathogens. Proceedings of the National Academy of Sciences of
the United States of America, 105 (3), 1091-1096.
doi:10.1073/pnas.0711215105
- Revers, F., Guiraud, T., Houvenaghel, M. C., Mauduit, T., Le Gall, O.,
& Candresse, T. (2003). Multiple Resistance Phenotypes to Lettuce
mosaic virus Among Arabidopsis thaliana Accessions. Molecular
Plant-Microbe Interactions, 16 (7), 608-616.
doi:10.1094/MPMI.2003.16.7.608
- Ribot, C., Hirsch, J., Balzergue, S., Tharreau, D., Notteghem, J. L.,
Lebrun, M. H., & Morel, J. B. (2008). Susceptibility of rice to the
blast fungus, Magnaporthe grisea. Journal of Plant Physiology,
165 (1), 114-124. doi:10.1016/j.jplph.2007.06.013
- Rose, L. E., Bittner-Eddy, P. D., Langley, C. H., Holub, E. B.,
Michelmore, R. W., & Beynon, J. L. (2004). The Maintenance of Extreme
Amino Acid Diversity at the Disease Resistance Gene,
<em>RPP13</em>, in
<em>Arabidopsis
thaliana</em>. Genetics, 166 (3),
1517-1527. doi:10.1534/genetics.166.3.1517 %J Genetics
- Roux, F., & Bergelson, J. (2016). Chapter Four - The Genetics
Underlying Natural Variation in the Biotic Interactions of Arabidopsis
thaliana: The Challenges of Linking Evolutionary Genetics and
Community Ecology. In V. Orgogozo (Ed.), Current Topics in
Developmental Biology (Vol. 119, pp. 111-156): Academic Press.
- Rozen, S., & Skaletsky, H. (1999). Primer3 on the WWW for General
Users and for Biologist Programmers. In S. Misener & S. A. Krawetz
(Eds.), Bioinformatics Methods and Protocols (pp. 365-386).
Totowa, NJ: Humana Press.
- Sagar, G. R., & Harper, J. L. (1964). Plantago Major L., P. Media L.
and P. Lanceolata L. Journal of Ecology, 52 (1), 189-221.
doi:10.2307/2257792
- Salvaudon, L., Giraud, T., & Shykoff, J. A. (2008). Genetic diversity
in natural populations: a fundamental component of plant-microbe
interactions. Current Opinion in Plant Biology, 11 (2), 135-143.
doi:10.1016/j.pbi.2008.02.002
- Sari, E., Bhadauria, V., Ramsay, L., Borhan, M. H., Lichtenzveig, J.,
Bett, K. E., . . . Banniza, S. (2018). Defense responses of lentil
(Lens culinaris) genotypes carrying non-allelic ascochyta blight
resistance genes to Ascochyta lentis infection. PLoS One,
13 (9), e0204124. doi:10.1371/journal.pone.0204124
- Sari, E., Bhadauria, V., Vandenberg, A., & Banniza, S. (2017).
Genotype-Dependent Interaction of Lentil Lines with Ascochyta lentis.Frontiers in Plant Science, 8 , 764. doi:10.3389/fpls.2017.00764
- Sarris, P. F., Cevik, V., Dagdas, G., Jones, J. D., & Krasileva, K.
V. (2016). Comparative analysis of plant immune receptor architectures
uncovers host proteins likely targeted by pathogens. BMC
Biology, 14 , 8. doi:10.1186/s12915-016-0228-7
- Schulz, M. H., Zerbino, D. R., Vingron, M., & Birney, E. (2012).
Oases: robust de novo RNA-seq assembly across the dynamic range of
expression levels. Bioinformatics, 28 (8), 1086-1092.
doi:10.1093/bioinformatics/bts094
- Seppey, M., Manni, M., & Zdobnov, E. M. (2019). BUSCO: Assessing
Genome Assembly and Annotation Completeness. In M. Kollmar (Ed.),Gene Prediction: Methods and Protocols (pp. 227-245). New York,
NY: Springer New York.
- Shang, X., Cao, Y., & Ma, L. (2017). Alternative Splicing in Plant
Genes: A Means of Regulating the Environmental Fitness of Plants.International Journal of Molecular Sciences, 18 (2).
doi:10.3390/ijms18020432
- Shao, Z. Q., Xue, J. Y., Wu, P., Zhang, Y. M., Wu, Y., Hang, Y. Y., .
. . Chen, J. Q. (2016). Large-Scale Analyses of Angiosperm
Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three
Anciently Diverged Classes with Distinct Evolutionary Patterns.Plant Physiology, 170 (4), 2095-2109. doi:10.1104/pp.15.01487
- Sheshukova, E. V., Komarova, T. V., Pozdyshev, D. V., Ershova, N. M.,
Shindyapina, A. V., Tashlitsky, V. N., . . . Dorokhov, Y. L. (2017).
The Intergenic Interplay between Aldose 1-Epimerase-Like Protein and
Pectin Methylesterase in Abiotic and Biotic Stress Control.Frontiers in Plant Science, 8 . doi:10.3389/fpls.2017.01646
- Soneson, C., Love, M. I., & Robinson, M. D. (2015). Differential
analyses for RNA-seq: transcript-level estimates improve gene-level
inferences. F1000Research, 4 , 1521.
doi:10.12688/f1000research.7563.2
- Srivastava, A., Sarkar, H., Malik, L., & Patro, R. (2016). Accurate,
Fast and Lightweight Clustering of de novo Transcriptomes using
Fragment Equivalence Classes. eprint arXiv:1604.03250 .
- Staiger, D., Korneli, C., Lummer, M., & Navarro, L. (2013). Emerging
role for RNA-based regulation in plant immunity. New
Phytologist, 197 (2), 394-404. doi:10.1111/nph.12022
- Stam, R., Silva-Arias, G. A., Nosenko, T., Scheikl, D., Hörger, A. C.,
Stephan, W., . . . Tellier, A. (2017). A small subset of NLR genes
drives local adaptation to pathogens in wild tomato. bioRxiv .
doi:10.1101/210559
- Steuernagel, B., Jupe, F., Witek, K., Jones, J. D., & Wulff, B. B.
(2015). NLR-parser: rapid annotation of plant NLR complements.Bioinformatics, 31 (10), 1665-1667.
doi:10.1093/bioinformatics/btv005
- Thompson, J. N., & Burdon, J. J. (1992). Gene-for-gene coevolution
between plants and parasites. Nature, 360 (6400), 121-125.
doi:10.1038/360121a0
- Thrall, P. H., Laine, A. L., Ravensdale, M., Nemri, A., Dodds, P. N.,
Barrett, L. G., & Burdon, J. J. (2012). Rapid genetic change
underpins antagonistic coevolution in a natural host-pathogen
metapopulation. Ecology Letters, 15 (5), 425-435.
doi:10.1111/j.1461-0248.2012.01749.x
- Tucker, A. E., Ackerman, M. S., Eads, B. D., Xu, S., & Lynch, M.
(2013). Population-genomic insights into the evolutionary origin and
fate of obligately asexual Daphnia pulex. Proceedings of the
National Academy of Sciences, 110 (39), 15740-15745.
doi:10.1073/pnas.1313388110
- Upson, J. L., Zess, E. K., Bialas, A., Wu, C. H., & Kamoun, S.
(2018). The coming of age of EvoMPMI: evolutionary molecular
plant-microbe interactions across multiple timescales. Current
Opinion in Plant Biology, 44 , 108-116. doi:10.1016/j.pbi.2018.03.003
- Wallstrom, S. V., Florez-Sarasa, I., Araujo, W. L., Aidemark, M.,
Fernandez-Fernandez, M., Fernie, A. R., . . . Rasmusson, A. G. (2014).
Suppression of the external mitochondrial NADPH dehydrogenase, NDB1,
in Arabidopsis thaliana affects central metabolism and vegetative
growth. Molecular Plant, 7 (2), 356-368. doi:10.1093/mp/sst115
- Walters, D. R., & McRoberts, N. (2006). Plants and biotrophs: a
pivotal role for cytokinins? Trends Plant Science, 11 (12),
581-586. doi:10.1016/j.tplants.2006.10.003
- Van de Weyer, A. L., Monteiro, F., Furzer, O. J., Nishimura, M. T.,
Cevik, V., Witek, K., . . . Bemm, F. (2019). A Species-Wide Inventory
of NLR Genes and Alleles in Arabidopsis thaliana. Cell, 178 (5),
1260-1272.e1214. doi:10.1016/j.cell.2019.07.038
- Van Ooijen, G., Mayr, G., Kasiem, M. M. A., Albrecht, M., Cornelissen,
B. J. C., & Takken, F. L. W. (2008). Structure–function analysis of
the NB-ARC domain of plant disease resistance proteins. Journal
of Experimental Botany, 59 (6), 1383-1397. doi:10.1093/jxb/ern045
- Varemo, L., Nielsen, J., & Nookaew, I. (2013). Enriching the gene set
analysis of genome-wide data by incorporating directionality of gene
expression and combining statistical hypotheses and methods.Nucleic Acids Research, 41 (8), 4378-4391.
doi:10.1093/nar/gkt111
- Wickham H. (2016). ggplot2: Elegant Graphics for Data Analysis.Springer-Verlag New York.
- Wiese, J., Kranz, T., & Schubert, S. (2004). Induction of pathogen
resistance in barley by abiotic stress. Plant Biology, 6 (5),
529-536. doi:10.1055/s-2004-821176
- Woolhouse, M. E. J., Taylor, L. H., & Haydon, D. T. (2001).
Population Biology of Multihost Pathogens. Science, 292 (5519),
1109-1112. doi:10.1126/science.1059026 %J Science
- Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., . . .
Wang, J. (2014). SOAPdenovo-Trans: de novo transcriptome assembly with
short RNA-Seq reads. Bioinformatics, 30 (12), 1660-1666.
doi:10.1093/bioinformatics/btu077
- Yang, J., Duan, G., Li, C., Liu, L., Han, G., Zhang, Y., & Wang, C.
(2019). The Crosstalks Between Jasmonic Acid and Other Plant Hormone
Signaling Highlight the Involvement of Jasmonic Acid as a Core
Component in Plant Response to Biotic and Abiotic Stresses.Frontiers in Plant Science, 10 . doi:10.3389/fpls.2019.01349
- Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood.Molecular Biology and Evolution, 24 (8), 1586-1591.
doi:10.1093/molbev/msm088
- Yu, G., Smith, D. K., Zhu, H., Guan, Y., Lam, T. T., & McInerny, G.
(2017). ggtree: anrpackage for visualization and annotation of
phylogenetic trees with their covariates and other associated data.Methods in Ecology and Evolution, 8 (1), 28-36.
doi:10.1111/2041-210x.12628
- Zhou, J., Sun, A., & Xing, D. (2013). Modulation of cellular redox
status by thiamine-activated NADPH oxidase confers Arabidopsis
resistance to Sclerotinia sclerotiorum. Journal of Experimental
Botany, 64 (11), 3261-3272. doi:10.1093/jxb/ert166
- Zhu, Y., Chen, H., Fan, J., Wang, Y., Li, Y., Chen, J., . . . Mundt,
C. C. (2000). Genetic diversity and disease control in rice.Nature, 406 (6797), 718-722. doi:10.1038/35021046