[1] Hulbert SH, Webb CA, Smith SM, Sun Q. Resistance gene complexes: Evolution and utilization. Annu Rev Phytopathol, 2001, 39: 285–312.
[2] 庄军, 刘志昕. 植物抗病基因的进化. 遗传, 2004, 26(6): 962–968.
[3] Flor HH. Current status of the gene-for-gene concept. Annu Rev Phytopathol, 1971, 9: 275–296.
[4] Kuang H, Woo SS, Meyers BC, Nevo E, Michelmore RW. Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell, 2004, 16(11): 2870–2894.
[5] Hammond-Kosack KE, Jones JDG. Plant disease resis¬tance genes. Annu Rev Plant Physiol Plant Mol Biol, 1997, 48: 575–607.
[6] Bai JF, Pennill LA, Ning JC, Lee SW, Ramalingam J, Webb CA, Zhao BY, Sun Q, Nelson JC, Leach JE, Hulbert SH. Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res, 2002, 12(12): 1871– 1884.
[7] Yue JX, Meyers BC, Chen JQ, Tian DC, Yang SH. Tracing the origin and evolutionary history of plant nucleo-tide-binding site-leucine-rich repeat (nbs-lrr) genes. New Phytol, 2012, 193(4): 1049–1063.
[8] Ameline-Torregrosa C, Wang BB, O'Bleness MS, Desh-pande S, Zhu H, Roe B, Young ND, Cannon SB. Identifi-cation and characterization of nucleotide-binding site-leucine- rich repeat genes in the model plant Medicago truncatula. Plant Physiol, 2008, 146(1): 5–21.
[9] 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] Yang SH, Zhang XH, Yue JX, Tian DC, Chen JQ. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics, 2008, 280(3): 187–198.
[11] Lin X, Zhang Y, Kuang H, Chen JJ. Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae. BMC Genomics, 2013, 14: 335.
[12] Xu X, Pan SK, Cheng SF, Zhang B, Mu DS, Ni PX, Zhang GU, Yang S, Li RQ, 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 DMA, Li GC, Yang Y, Kuang H, Hu Q, Xiong XY, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang ZH, Liang CB, He J, Li Y, He Y, Xu JF, Zhang YJ, Xie BY, Du YC, Qu DY, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sønderkaer M, Iovene M, Torres GA, Jiang JM, Veilleux RE, Bachem CWB, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert BL, Goverse A, van Ham RCHJ, Visser RGF. Genome sequence and analysis of the tuber crop potato. Nature, 2011, 475(7355): 189–195.
[13] Xu Q, Chen LL, Ruan XA, Chen DJ, Zhu DA, Chen CL, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen JJ, Gao S, Xing F, Lan H, Chang JW, Ge XH, Lei Y, Hu Q, Miao Y, Wang L, Xiao SX, Biswas MK, Zeng WF, Guo F, Cao HB, Yang XM, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang ZH, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan YJ. The draft genome of sweet orange (citrus sinensis). Nat Genet, 2013, 45(1): 59–66.
[14] Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W, Martin F. Genome-wide identification of nbs resistance genes in Populus trichocarpa. Plant Mol Biol, 2008, 66(6): 619–636.
[15] Li J, Ding J, Zhang W, Zhang YL, Tang P, Chen JQ, Tian DC, Yang SH. Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol Genet Genomics, 2010, 283(5): 427–438.
[16] Luo S, Zhang Y, Hu Q, Chen JJ, Li KP, Lu C, Liu H, Wang W, Kuang H. Dynamic nucleotide-binding site and leucine- rich repeat-encoding genes in the grass family. Plant Physiol, 2012, 159(1): 197–210.
[17] Jia JZ, Zhao SC, Kong XY, Li YR, Zhao GY, He WM, Appels R, Pfeifer M, Tao Y, Zhang XY, Jing RL, Zhang C, Ma YZ, Gao LF, Gao C, Spannagl M, Mayer KF, Li D, Pan SK, Zheng FY, Hu Q, Xia XC, Li JW, Liang QS, Chen J, Wicker T, Gou CY, Kuang H, He GJ, Luo YD, Keller B, Xia QJ, Lu P, Wang JY, Zou HF, Zhang R, Xu J, Gao J, Middleton C, Quan ZW, Liu GM, Yang HM, Liu X, He ZH, Mao L, Wang J. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 2013, 496(7443): 91–95.
[18] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (torr. & gray). Science, 2006, 313(5793): 1596–1604.
[19] 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, Bruyère 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, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 2007, 449(7161): 463–467.
[20] Ming R, Hou SB, Feng Y, Yu QY, 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, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang XY, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei HR, Irikura B, Paidi M, Jiang N, Zhang WL, Presting G, Windsor A, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Li YJ, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang JM, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya linnaeus). Nature, 2008, 452(7190): 991–996.
[21] Huang SW, Li RQ, Zhang ZH, Li L, Gu XF, Fan W, Lucas WJ, Wang XW, Xie BY, Ni PX, Ren YY, Zhu HM, Li J, Lin K, Jin WW, Fei ZJ, Li GC, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia ZQ, Ren Y, Tian G, Lu Y, Ruan J, Qian WB, Wang MW, Huang QF, Li B, Xuan ZL, Cao JJ, Asan, Wu ZG, Zhang JB, Cai QL, Bai YQ, Zhao BW, Han YH, Li Y, Li XF, Wang SH, Shi QX, Liu SQ, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng ZC, Zhang SP, Wu J, Yang YY, Kang HX, Li M, Liang HQ, Ren XL, Shi ZB, Wen M, Jian M, Yang HL, Zhang GJ, Yang ZT, Chen R, Ma LJ, Liu H, Zhou Y, Zhao J, Fang XD, Fang L, Liu DY, Zheng HK, Zhang Y, Qin N, Li Z, Yang GH, Yang S, Bolund L, Kristiansen K, Li SC, Zhang XQ, Wang J, Sun RF, Zhang BX, Jiang SZ, Du YC. The genome of the cucumber, Cucumis sativus L. Nat Genet, 2009, 41(12): 1275–1281.
[22] Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez- Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente- Galdos B, Melé M, Yang LM, Weng YQ, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdo¬mènech P. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA, 2012, 109(29): 11872–11877.
[23] Guo SG, Zhang JG, Sun HH, Salse J, Lucas WJ, Zhang HY, Zheng Y, Mao LY, Ren Y, Wang ZW, Min JM, Guo XS, Murat F, Ham BK, Zhang ZL, Gao S, Huang MY, Xu YM, Zhong SL, Bombarely A, Mueller LA, Zhao H, He HJ, Zhang Y, Huang SW, Tan T, Pang E, Lin K, Hu Q, Kuang H, Ni PX, Wang B, Liu JG, Kou QH, Hou WJ, Zou XH, Jiang J, Gong GY, Klee K, Schoof H, Huang Y, Hu XS, Dong SS, Liang DQ, Wang J, Wu K, Xia Y, Zhao X, Zheng ZQ, Xing M, Liang XM, Huang BQ, Lv T, Yin Y, Yi HP, Li RQ, Wu MZ, Levi A, Zhang XP, Giovannoni JJ, Li YF, Fei ZJ, Xu Y. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet, 2013, 45(1): 51–58.
[24] Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo NX, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012, 491(7426): 705–710.
[25] Tian DC, Araki H, Stahl E, Bergelson J, Kreitman M. Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci USA, 2002, 99(17): 11525–11530.
[26] Mondragón-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.
[27] Dodds PN, Lawrence GJ, Ellis JG. Contrasting modes of evolution acting on the complex N locus for rust resistance in flax. Plant J, 2001, 27(5): 439–453.
[28] 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.
[29] Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof MA, Young ND, Innes RW. Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine. Plant Physiol, 2012, 159(1): 336–354.
[30] Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics, 2004, 271(4): 402–415.
[31] Yu JY, Tehrim S, Zhang FQ, Tong CB, Huang JY, Cheng XH, Dong CH, Zhou Y, Q Qin R, Hua W, Liu SY. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis Thaliana. BMC Genomics, 2014, 15: 3.
[32] Gale MD, Devos KM. Plant comparative genetics after 10 years. Science, 1998, 282(5389): 656–659.
[33] Ratnaparkhe MB, Wang XY, Li JP, Compton RO, Rainville LK, Lemke C, Kim C, Tang HB, 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.
[34] Yang S, Feng Z, Zhang X, Jiang K, Jin X, Hang Y, Chen JQ, Tian D. Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol Biol, 2006, 62(1–2): 181–193.
[35] Shen JD, Araki H, Chen LL, Chen JQ, Tian DC. Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics, 2006, 172(2): 1243–1250.
[36] Nei M, Rooney AP. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet, 2005, 39: 121–152.
[37] Luo S, Peng J, Li K, Wang M, Kuang H. Contrasting evolutionary patterns of the Rp1 resistance gene family in different species of poaceae. Mol Biol Evol, 2011, 28(1): 313–325.
[38] Kuang H, Caldwell KS, Meyers BC, Michelmore RW. Frequent sequence exchanges between homologs of Rpp8 in Arabidopsis are not necessarily associated with genomic proximity. Plant J, 2008, 54(1): 69–80.
[39] Huang SW, van der Vossen EA, Kuang H, Vleeshouwers VGAA, Zhang NW, Borm TJA, van Eck HJ, Baker B, Jacobsen E, Visser RGF. Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. Plant J, 2005, 42(2): 251–261.
[40] Wei HL, Li W, Sun XW, Zhu SJ, Zhu J. Systematic analysis and comparison of nucleotide-binding site disease resistance genes in a diploid cotton Gossypium raimondii. PLoS ONE, 2013, 8(8): e68435.
[41] Kuang H, van Eck HJ, Sicard D, Michelmore R, Nevo E. Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster. Genetics, 2008, 178(3): 1547–1558.
[42] Smith SM, Pryor AJ, Hulbert SH. Allelic and haplotypic diversity at the Rp1 rust resistance locus of maize. Genetics, 2004, 167(4): 1939–1947.
[43] Webb CA, Richter TE, Collins NC, Nicolas M, Trick HN, Pryor T, Hulbert SH. Genetic and molecular characterization of the maize Rp3 rust resistance locus. Genetics, 2002, 162(1): 381–394.
[44] Henk AD, Warren RF, Innes RW. A new Ac-like transposon of Arabidopsis is associated with a deletion of the Rps5 disease resistance gene. Genetics, 1999, 151(4): 1581–1589.
[45] Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun HY, Kumar P, Baker B. Microrna regulation of plant innate immune receptors. Proc Natl Acad Sci USA, 2012, 109(5): 1790–1795.
[46] Zhai JX, Jeong DH, De Paoli E, Park S, Rosen BD, Li YP, González AJ, Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier DJ, Meyers BC. Micrornas as master regulators of the plant NB-LRR defense gene family via the production of phased, trans- acting sirnas. Genes Dev, 2011, 25(23): 2540–2553.
[47] Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC. A microrna superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell, 2012, 24(3): 859–874.
[48] Fei QL, Xia R, Meyers BC. Phased, secondary, small interfering rnas in posttranscriptional regulatory networks. Plant Cell, 2013, 25(7): 2400–2415.
[49] Tian D, Traw MB, Chen JQ, Kreitman M, Bergelson J. Fitness costs of r-gene-mediated resistance in Arabidopsis thaliana. Nature, 2003, 423(6935): 74–77. |