Jones JD, Dangl JL: The plant immune system. Nature. 2006, 444 (7117): 323-329. 10.1038/nature05286.
CAS
PubMed
Google Scholar
Chinchilla D, Bauer Z, Regenass M, Boller T, Felix G: The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell. 2006, 18 (2): 465-476. 10.1105/tpc.105.036574.
CAS
PubMed Central
PubMed
Google Scholar
Zipfel C, Robatzek S: Pathogen-associated molecular pattern-triggered immunity: veni, vidi…?. Plant Physiol. 2010, 154 (2): 551-554. 10.1104/pp.110.161547.
CAS
PubMed Central
PubMed
Google Scholar
Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu JL, Huckelhoven R, Stein M, Freialdenhoven A, Somerville SC, Schulze-Lefert P: SNARE-protein-mediated disease resistance at the plant cell wall. Nature. 2003, 425 (6961): 973-977. 10.1038/nature02076.
CAS
PubMed
Google Scholar
Schwessinger B, Zipfel C: News from the frontline: recent insights into PAMP-triggered immunity in plants. Curr Opin Plant Biol. 2008, 11 (4): 389-395. 10.1016/j.pbi.2008.06.001.
CAS
PubMed
Google Scholar
Hann DR, Dominguez-Ferreras A, Motyka V, Dobrev PI, Schornack S, Jehle A, Felix G, Chinchilla D, Rathjen JP, Boller T: The Pseudomonas type III effector HopQ1 activates cytokinin signaling and interferes with plant innate immunity. New Phytol. 2013, n/a-n/a.
Google Scholar
Van der Biezen EA, Jones JD: Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem Sci. 1998, 23 (12): 454-456. 10.1016/S0968-0004(98)01311-5.
CAS
PubMed
Google Scholar
Vleeshouwers VG, Raffaele S, Vossen JH, Champouret N, Oliva R, Segretin ME, Rietman H, Cano LM, Lokossou A, Kessel G, Pel MA, Kamoun S: Understanding and exploiting late blight resistance in the age of effectors. Annu Rev Phytopathol. 2011, 49: 507-531. 10.1146/annurev-phyto-072910-095326.
CAS
PubMed
Google Scholar
Ballvora A, Ercolano MR, Weiss J, Meksem K, Bormann CA, Oberhagemann P, Salamini F, Gebhardt C: The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes. Plant J. 2002, 30 (3): 361-371. 10.1046/j.1365-313X.2001.01292.x.
CAS
PubMed
Google Scholar
Young ND: The genetic architecture of resistance. Curr Opin Plant Biol. 2000, 3 (4): 285-290. 10.1016/S1369-5266(00)00081-9.
CAS
PubMed
Google Scholar
Guo YL, Fitz J, Schneeberger K, Ossowski S, Cao J, Weigel D: Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. Plant Physiol. 2011, 157 (2): 757-769. 10.1104/pp.111.181990.
CAS
PubMed Central
PubMed
Google Scholar
Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, Beynon JL, Daniels MJ, Holub EB, Jones JD: Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell. 1998, 10 (11): 1847-1860. 10.1105/tpc.10.11.1847.
CAS
PubMed Central
PubMed
Google Scholar
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW: Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003, 15 (4): 809-834. 10.1105/tpc.009308.
CAS
PubMed Central
PubMed
Google Scholar
McHale L, Tan X, Koehl P, Michelmore RW: Plant NBS-LRR proteins: adaptable guards. Genome Biol. 2006, 7 (4): 212-10.1186/gb-2006-7-4-212.
PubMed Central
PubMed
Google Scholar
Maekawa T, Kufer TA, Schulze-Lefert P: NLR functions in plant and animal immune systems: so far and yet so close. Nat Immunol. 2011, 12 (9): 817-826. 10.1038/ni.2083.
CAS
PubMed
Google Scholar
Boisson B, Giglione C, Meinnel T: Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote. J Biol Chem. 2003, 278 (44): 43418-43429. 10.1074/jbc.M307321200.
CAS
PubMed
Google Scholar
Warren RF, Henk A, Mowery P, Holub E, Innes RW: A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes. Plant Cell. 1998, 10 (9): 1439-1452. 10.1105/tpc.10.9.1439.
CAS
PubMed Central
PubMed
Google Scholar
Deslandes L, Olivier J, Peeters N, Feng DX, Khounlotham M, Boucher C, Somssich I, Genin S, Marco Y: Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc Natl Acad Sci. 2003, 100 (13): 8024-8029. 10.1073/pnas.1230660100.
CAS
PubMed Central
PubMed
Google Scholar
Narusaka M, Shirasu K, Noutoshi Y, Kubo Y, Shiraishi T, Iwabuchi M, Narusaka Y: RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens. Plant J. 2009, 60 (2): 218-226. 10.1111/j.1365-313X.2009.03949.x.
CAS
PubMed
Google Scholar
Yang H, Shi Y, Liu J, Guo L, Zhang X, Yang S: A mutant CHS3 protein with TIR-NB-LRR-LIM domains modulates growth, cell death and freezing tolerance in a temperature-dependent manner in Arabidopsis. Plant J. 2010, 63 (2): 283-296. 10.1111/j.1365-313X.2010.04241.x.
CAS
PubMed
Google Scholar
Kato H, Shida T, Komeda Y, Saito T, Kato A: Overexpression of the Activated Disease Resistance 1-like1 (ADR1-L1) Gene Results in a Dwarf Phenotype and Activation of Defense-Related Gene Expression in Arabidopsis thaliana. J Plant Biol. 2011, 54 (3): 172-179. 10.1007/s12374-011-9153-z.
CAS
Google Scholar
Xiao S, Charoenwattana P, Holcombe L, Turner JG: The Arabidopsis genes RPW8.1 and RPW8.2 confer induced resistance to powdery mildew diseases in tobacco. Mol Plant Microbe Interact. 2003, 16 (4): 289-294. 10.1094/MPMI.2003.16.4.289.
CAS
PubMed
Google Scholar
Xiao S, Calis O, Patrick E, Zhang G, Charoenwattana P, Muskett P, Parker JE, Turner JG: The atypical resistance gene, RPW8, recruits components of basal defence for powdery mildew resistance in Arabidopsis. Plant J. 2005, 42 (1): 95-110. 10.1111/j.1365-313X.2005.02356.x.
CAS
PubMed
Google Scholar
Dangl JL, Jones JD: Plant pathogens and integrated defence responses to infection. Nature. 2001, 411 (6839): 826-833. 10.1038/35081161.
CAS
PubMed
Google Scholar
van Ooijen G, Mayr G, Kasiem MM, Albrecht M, Cornelissen BJ, Takken FL: Structure-function analysis of the NB-ARC domain of plant disease resistance proteins. J Exp Bot. 2008, 59 (6): 1383-1397. 10.1093/jxb/ern045.
CAS
PubMed
Google Scholar
Boller T, Felix G: A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol. 2009, 60 (1): 379-406. 10.1146/annurev.arplant.57.032905.105346.
CAS
PubMed
Google Scholar
Tameling WIL, Vossen JH, Albrecht M, Lengauer T, Berden JA, Haring MA, Cornelissen BJC, Takken FLW: Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol. 2006, 140 (4): 1233-1245. 10.1104/pp.105.073510.
CAS
PubMed Central
PubMed
Google Scholar
Takken FLW, Goverse A: How to build a pathogen detector: structural basis of NB-LRR function. Curr Opin Plant Biol. 2012, 15 (4): 375-384. 10.1016/j.pbi.2012.05.001.
CAS
PubMed
Google Scholar
Bhattacharyya MK: RPSk-1 gene family, nucleotide sequences and uses thereof. Google Patents. 2007
Google Scholar
Cannon SB, Mitra A, Baumgarten A, Young ND, May G: The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004, 4 (1): 10-10.1186/1471-2229-4-10.
PubMed Central
PubMed
Google Scholar
Mondragon-Palomino M, Meyers BC, Michelmore RW, Gaut BS: Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 2002, 12 (9): 1305-1315. 10.1101/gr.159402.
CAS
PubMed Central
PubMed
Google Scholar
Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Soltis DE, Soltis PS, Stevens PF, Anderberg AA, Moore MJ, Olmstead RG, Rudall PJ, Sytsma KJ, Tank DC, Wurdack K, Xiang JQY, Zmarzty S, Grp AP: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc. 2009, 161 (2): 105-121.
Google Scholar
Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK, Soltis DE, Depamphilis CW: A genome triplication associated with early diversification of the core eudicots. Genome Biol. 2012, 13 (1): R3-10.1186/gb-2012-13-1-r3.
PubMed Central
PubMed
Google Scholar
Lyons E, Freeling M: How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 2008, 53 (4): 661-673. 10.1111/j.1365-313X.2007.03326.x.
CAS
PubMed
Google Scholar
Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool. 1970, 19 (2): 99-113. 10.2307/2412448.
CAS
PubMed
Google Scholar
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M: Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 2008, 148 (4): 1772-1781. 10.1104/pp.108.124867.
CAS
PubMed Central
PubMed
Google Scholar
Ohno S: Evolution by Gene Duplication, Volume 1970. 1970, New York: Springer Publishing Group, 1
Google Scholar
Freeling M: Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol. 2009, 60: 433-453. 10.1146/annurev.arplant.043008.092122.
CAS
PubMed
Google Scholar
Bowers JE, Chapman BA, Rong J, Paterson AH: Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003, 422 (6930): 433-438. 10.1038/nature01521.
CAS
PubMed
Google Scholar
Wolfe K: Robustness—it's not where you think it is. Nat Genet. 2000, 25 (1): 3-4. 10.1038/75560.
CAS
PubMed
Google Scholar
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, de Pamphilis CW: Ancestral polyploidy in seed plants and angiosperms. Nature. 2011, 473 (7345): 97-100. 10.1038/nature09916.
CAS
PubMed
Google Scholar
Schranz ME, Mohammadin S, Edger PP: Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Curr Opin Plant Biol. 2012, 15 (2): 147-153. 10.1016/j.pbi.2012.03.011.
PubMed
Google Scholar
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandakova T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M: An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet. 2013, 45 (8): 891-898. 10.1038/ng.2684.
CAS
PubMed
Google Scholar
Barker MS, Vogel H, Schranz ME: Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biol Evol. 2009, 1: 391-399.
PubMed Central
PubMed
Google Scholar
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, et al: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008, 452 (7190): 991-996. 10.1038/nature06856.
CAS
PubMed Central
PubMed
Google Scholar
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K: Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. Mol Biol Evol. 2012, 29 (12): 3793-3806. 10.1093/molbev/mss183.
CAS
PubMed
Google Scholar
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, et al: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007, 449 (7161): 463-467. 10.1038/nature06148.
CAS
PubMed
Google Scholar
Tang H, Lyons E: Unleashing the genome of brassica rapa. Front Plant Sci. 2012, 3: 172-
CAS
PubMed Central
PubMed
Google Scholar
Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, Bian C, Chen J, Fan G, Kaufmann K, Hall JC, Becker A, Brautigam A, Weber AP, Shi C, Zheng Z, Li W, Lv M, Tao Y, Wang J, Zou H, Quan Z, Hibberd JM, Zhang G, Zhu XG, Xu X, et al: The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. Plant Cell. 2013, 25 (8): 2813-2830. 10.1105/tpc.113.113480.
CAS
PubMed Central
PubMed
Google Scholar
Tomato Genome C: The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012, 485 (7400): 635-641. 10.1038/nature11119.
Google Scholar
Fang L, Cheng F, Wu J, Wang X: The impact of genome triplication on tandem gene evolution in Brassica rapa. Front Plant Sci. 2012, 3: 261-
CAS
PubMed Central
PubMed
Google Scholar
Kane J, Freeling M, Lyons E: The evolution of a high copy gene array in Arabidopsis. J Mol Evol. 2010, 70 (6): 531-544. 10.1007/s00239-010-9350-2.
CAS
PubMed Central
PubMed
Google Scholar
Rizzon C, Ponger L, Gaut BS: Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol. 2006, 2 (9): e115-10.1371/journal.pcbi.0020115.
PubMed Central
PubMed
Google Scholar
Leister D: Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene. TIG. 2004, 20 (3): 116-122. 10.1016/j.tig.2004.01.007.
CAS
PubMed
Google Scholar
Parniske M, Wulff BB, Bonnema G, Thomas CM, Jones DA, Jones JD: Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1. Mol Plant Microbe Interact. 1999, 12 (2): 93-102. 10.1094/MPMI.1999.12.2.93.
CAS
PubMed
Google Scholar
Bellieny-Rabelo D, Oliveira AE, Venancio TM: Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PLoS One. 2013, 8 (2): e55127-10.1371/journal.pone.0055127.
CAS
PubMed Central
PubMed
Google Scholar
Thomas BC, Pedersen B, Freeling M: Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 2006, 16 (7): 934-946. 10.1101/gr.4708406.
CAS
PubMed Central
PubMed
Google Scholar
Freeling M, Thomas BC: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 2006, 16 (7): 805-814. 10.1101/gr.3681406.
CAS
PubMed
Google Scholar
Schnable JC, Springer NM, Freeling M: Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A. 2011, 108 (10): 4069-4074. 10.1073/pnas.1101368108.
CAS
PubMed Central
PubMed
Google Scholar
Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric Schranz M: Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biol Evol. 2013, 5 (11): 2155-2173. 10.1093/gbe/evt162.
CAS
PubMed Central
PubMed
Google Scholar
Paterson AH, Freeling M, Tang H, Wang X: Insights from the comparison of plant genome sequences. Annu Rev Plant Biol. 2010, 61 (1): 349-372. 10.1146/annurev-arplant-042809-112235.
CAS
PubMed
Google Scholar
De Bodt S, Maere S, Van de Peer Y: Genome duplication and the origin of angiosperms. Trends Ecol Evol. 2005, 20 (11): 591-597. 10.1016/j.tree.2005.07.008.
PubMed
Google Scholar
Irish VF, Litt A: Flower development and evolution: gene duplication, diversification and redeployment. Curr Opin Genet Dev. 2005, 15 (4): 454-460. 10.1016/j.gde.2005.06.001.
CAS
PubMed
Google Scholar
Fawcett JA, Maere S, Van de Peer Y: Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A. 2009, 106 (14): 5737-5742. 10.1073/pnas.0900906106.
CAS
PubMed Central
PubMed
Google Scholar
Richly E, Kurth J, Leister D: Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol Evol. 2002, 19 (1): 76-84. 10.1093/oxfordjournals.molbev.a003984.
CAS
PubMed
Google Scholar
Yang S, Zhang X, Yue JX, Tian D, Chen JQ: Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics. 2008, 280 (3): 187-198. 10.1007/s00438-008-0355-0.
CAS
PubMed
Google Scholar
Chen Q, Han Z, Jiang H, Tian D, Yang S: Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J Mol Evol. 2010, 70 (2): 137-148. 10.1007/s00239-009-9316-4.
CAS
PubMed
Google Scholar
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E: The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2008, 36 (Database issue): D1009-D1014.
CAS
PubMed Central
PubMed
Google Scholar
Mun JH, Yu HJ, Park S, Park BS: Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Genet Genomics. 2009, 282 (6): 617-631. 10.1007/s00438-009-0492-0.
CAS
PubMed Central
PubMed
Google Scholar
Yu J, Tehrim S, Zhang F, Tong C, Huang J, Cheng X, Dong C, Zhou Y, Qin R, Hua W: Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. BMC Genomics. 2014, 15 (1): 3-10.1186/1471-2164-15-3.
PubMed Central
PubMed
Google Scholar
Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000, 10 (4): 516-522. 10.1101/gr.10.4.516.
CAS
PubMed Central
PubMed
Google Scholar
Schranz ME, Mitchell-Olds T: Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell. 2006, 18 (5): 1152-1165. 10.1105/tpc.106.041111.
CAS
PubMed Central
PubMed
Google Scholar
Porter BW, Paidi M, Ming R, Alam M, Nishijima WT, Zhu YJ: Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol Genet Genomics. 2009, 281 (6): 609-626. 10.1007/s00438-009-0434-x.
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410. 10.1016/S0022-2836(05)80360-2.
CAS
PubMed
Google Scholar
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res. 2004, 32 (Database issue): D138-D141.
CAS
PubMed Central
PubMed
Google Scholar
Hermoso A, Vlasova A, Sanseverino W, D’Alessandro R, Andolfo G, Frusciante L, Roma G, Ercolano M, Lowy E: The Plant Resistance Gene Database (PRGdb): a Wiki-based system for the annotation of R-genes. IWBBIO Proc. 2009, http://iwbbio.ugr.es/papers/iwbbio_112.pdf,
Google Scholar
Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I: Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics. 2012, 13 (1): 75-10.1186/1471-2164-13-75.
CAS
PubMed Central
PubMed
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009, 37 (Web Server issue): W202-W208.
CAS
PubMed Central
PubMed
Google Scholar
Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JD: Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J. 2013, 76 (3): 530-544. 10.1111/tpj.12307.
CAS
PubMed Central
PubMed
Google Scholar
Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA: Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007, 4 (11): 903-905. 10.1038/nmeth1111.
CAS
PubMed
Google Scholar
Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR: Genome-wide in situ exon capture for selective resequencing. Nat Genet. 2007, 39 (12): 1522-1527. 10.1038/ng.2007.42.
CAS
PubMed
Google Scholar
Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J: Targeted enrichment strategies for next-generation plant biology. Am J Bot. 2012, 99 (2): 291-311. 10.3732/ajb.1100356.
CAS
PubMed
Google Scholar
Andolfo G, Sanseverino W, Rombauts S, Van de Peer Y, Bradeen JM, Carputo D, Frusciante L, Ercolano MR: Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol. 2013, 197 (1): 223-237. 10.1111/j.1469-8137.2012.04380.x.
CAS
PubMed
Google Scholar
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M: Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics. 2011, 12: 102-10.1186/1471-2105-12-102.
PubMed Central
PubMed
Google Scholar
Hurst LD: The Ka/Ks ratio: diagnosing the form of sequence evolution. TIG. 2002, 18 (9): 486-10.1016/S0168-9525(02)02722-1.
PubMed
Google Scholar
Tan X, Meyers BC, Kozik A, West MA, Morgante M, St Clair DA, Bent AF, Michelmore RW: Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol. 2007, 7 (1): 56-10.1186/1471-2229-7-56.
PubMed Central
PubMed
Google Scholar
Navarro L, Zipfel C, Rowland O, Keller I, Robatzek S, Boller T, Jones JD: The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesis. Plant Physiol. 2004, 135 (2): 1113-1128. 10.1104/pp.103.036749.
CAS
PubMed Central
PubMed
Google Scholar
Lewis JD, Wu R, Guttman DS, Desveaux D: Allele-specific virulence attenuation of the Pseudomonas syringae HopZ1a type III effector via the Arabidopsis ZAR1 resistance protein. PLoS Genet. 2010, 6 (4): e1000894-10.1371/journal.pgen.1000894.
PubMed Central
PubMed
Google Scholar
Bonardi V, Cherkis K, Nishimura MT, Dangl JL: A new eye on NLR proteins: focused on clarity or diffused by complexity?. Curr Opin Immunol. 2012, 24 (1): 41-50. 10.1016/j.coi.2011.12.006.
CAS
PubMed Central
PubMed
Google Scholar
Wang W, Zhang Y, Wen Y, Berkey R, Ma X, Pan Z, Bendigeri D, King H, Zhang Q, Xiao S: A comprehensive mutational analysis of the Arabidopsis resistance protein RPW8.2 reveals key amino acids for defense activation and protein targeting. Plant Cell. 2013, 25 (10): 4242-4261. 10.1105/tpc.113.117226.
CAS
PubMed Central
PubMed
Google Scholar
Bonardi V, Tang S, Stallmann A, Roberts M, Cherkis K, Dangl JL: Expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors. Proc Natl Acad Sci U S A. 2011, 108 (39): 16463-16468. 10.1073/pnas.1113726108.
CAS
PubMed Central
PubMed
Google Scholar
Roberts M, Tang S, Stallmann A, Dangl JL, Bonardi V: Genetic requirements for signaling from an autoactive plant NB-LRR intracellular innate immune receptor. PLoS Genet. 2013, 9 (4): e1003465-10.1371/journal.pgen.1003465.
CAS
PubMed Central
PubMed
Google Scholar
Uitdewilligen JG, Wolters AM, D’Hoop BB, Borm TJ, Visser RG, van Eck HJ: A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One. 2013, 8 (5): e62355-10.1371/journal.pone.0062355.
CAS
PubMed Central
PubMed
Google Scholar
Michelmore RW, Meyers BC: Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 1998, 8 (11): 1113-1130.
CAS
PubMed
Google Scholar
Ratnaparkhe MB, Wang X, Li J, Compton RO, Rainville LK, Lemke C, Kim C, Tang H, Paterson AH: Comparative analysis of peanut NBS‒LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. New Phytol. 2011, 192 (1): 164-178. 10.1111/j.1469-8137.2011.03800.x.
PubMed
Google Scholar
Collier SM, Hamel LP, Moffett P: Cell death mediated by the N-terminal domains of a unique and highly conserved class of NB-LRR protein. Mol Plant Microbe Interact. 2011, 24 (8): 918-931. 10.1094/MPMI-03-11-0050.
CAS
PubMed
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS: Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012, 40 (Database issue): D1178-D1186.
CAS
PubMed Central
PubMed
Google Scholar
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL: The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011, 43 (5): 476-481. 10.1038/ng.807.
PubMed Central
PubMed
Google Scholar
Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing RA, Mitchell-Olds T, Schumaker KS, Wang X: The reference genome of the halophytic plant Eutrema salsugineum. Front Plant Sci. 2013, 4: 46-
CAS
PubMed Central
PubMed
Google Scholar
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Tong C, Song C, Duran C: The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011, 43 (10): 1035-1039. 10.1038/ng.919.
CAS
PubMed
Google Scholar
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, et al: The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013, 45 (1): 59-66.
CAS
PubMed
Google Scholar
Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Potato Genome Sequencing C, et al: Genome sequence and analysis of the tuber crop potato. Nature. 2011, 475 (7355): 189-195. 10.1038/nature10158.
CAS
PubMed
Google Scholar
Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB: A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact. 2012, 25 (12): 1523-1530. 10.1094/MPMI-06-12-0148-TA.
CAS
PubMed
Google Scholar
Haas BJ, Delcher AL, Wortman JR, Salzberg SL: DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics. 2004, 20 (18): 3643-3646. 10.1093/bioinformatics/bth397.
CAS
PubMed
Google Scholar
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24 (8): 1586-1591. 10.1093/molbev/msm088.
CAS
PubMed
Google Scholar
Woodhouse MR, Tang H, Freeling M: Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell. 2011, 23 (12): 4241-4253. 10.1105/tpc.111.093567.
CAS
PubMed Central
PubMed
Google Scholar
Zdobnov EM, Apweiler R: InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001, 17 (9): 847-848. 10.1093/bioinformatics/17.9.847.
CAS
PubMed
Google Scholar
Offord V, Werling D: LRRfinder2.0: a webserver for the prediction of leucine-rich repeats. Innate Immun. 2013, 19 (4): 398-402. 10.1177/1753425912465661.
PubMed
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30 (14): 3059-3066. 10.1093/nar/gkf436.
CAS
PubMed Central
PubMed
Google Scholar
Suyama M, Torrents D, Bork P: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006, 34 (Web Server issue): W609-W612.
CAS
PubMed Central
PubMed
Google Scholar
Zhang Z, Li J, Zhao X-Q, Wang J, Wong GK-S, Yu J: KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 2006, 4: 259-263. 10.1016/S1672-0229(07)60007-2.
CAS
PubMed
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19 (9): 1639-1645. 10.1101/gr.092759.109.
CAS
PubMed Central
PubMed
Google Scholar