Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity

BMC Genomics

Volumn 10, Issue , 2009, Pages 415-

  Ashraf, Nasheeman ^a   Ghai, Deepali ^a   Barman, Pranjan ^a   Basu, Swaraj ^a   Gangisetty, Nagaraju ^a   Mandal, Mihir K ^a   Chakraborty, Niranjan ^a   Datta, Asis ^a   Chakraborty, Subhra ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE BINDING PROTEIN; TRANSCRIPTOME; PLANT DNA;

ARTICLE; CELL CYCLE; CELL TRANSPORT; CHICKPEA; COMPARATIVE STUDY; CONTROLLED STUDY; CYTOSKELETON; DNA METABOLISM; ENERGY METABOLISM; EXPRESSED SEQUENCE TAG; FUSARIUM; GENE EXPRESSION; GENE SEQUENCE; GENETIC DATABASE; GENOTYPE; HOMEOSTASIS; HORMONE RESPONSE; IMMUNE RESPONSE; IMMUNITY; LEGUME; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PLANT GENE; PLANT GENETICS; PLANT GENOME; PLANT ROOT; PLANT STRESS; PREDICTION; PROTEIN PROCESSING; RNA PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM; UNINDEXED SEQUENCE; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTIG MAPPING; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; IMMUNOLOGY; MICROBIOLOGY; PLANT DISEASE;

CICER ARIETINUM; FUSARIUM;

CICER; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTIG MAPPING; DATABASES, GENETIC; DNA, PLANT; EXPRESSED SEQUENCE TAGS; FUSARIUM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; GENOTYPE; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 70350438617     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-415     Document Type: Article

References (109)

1. White JA, Todd J, Newman T, Focks N, Girke T, de Ilarduya M, Jaworski JG, Ohlrogge JB, Benning C. A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol 2000, 124:1582-1594. 11115876, 10.1104/pp.124.4.1582, 59857.
2. Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 1999, 9:950-959. 10523523, 10.1101/gr.9.10.950, 310820.
3. Jantasuriyarat C, Gowda M, Haller K, Hatfield J, Lu G, Stahlberg E, Zhou B, Li H, Kim H, Yu Y, Dean RA, Wing RA, Soderlund C, Wang GL. Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiol 2005, 138:105-115. 15888683, 10.1104/pp.104.055624, 1104166.
4. Ramírez M, Graham MA, Blanco-López L, Silvente S, Medrano-Soto A, Blair MW, Hernández G, Vance CP, Lara M. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 2005, 137:1211-1227. 15824284, 10.1104/pp.104.054999, 1088315.
5. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB. A global assembly of cotton ESTs. Genome Res 2006, 16:441-450. 16478941, 10.1101/gr.4602906, 1415220.
6. Takabatake T, Ishihara H, Ohmachi Y, Tanaka I, Nakamura MM, Fujikawa K, Hirouchi T, Kakinuma S, Shimada Y, Oghiso Y, Tanaka K. Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome. Nucleic Acids Res 2008, 36:e59. 18450814, 10.1093/nar/gkn235, 2425471.
7. Melamed D, Pnueli L, Arava Y. Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 2008, 14:1337-1351. 18495938, 10.1261/rna.864908, 2441982.
8. LeBlanc JC, Gonçalves ER, Mohn WW. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 2008, 74:2627-2636. 18326668, 10.1128/AEM.02711-07, 2394902.
9. Wellmer F, Alves-Ferreira M, Dubois A, Riechmann JL, Meyerowitz EM. Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genetics 2006, 2:1012-1024.
10. Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE 2007, 2:e1235. 18043742, 10.1371/journal.pone.0001235, 2084198.
11. Haridas V, Higuchi M, Jaytilake GS, Baily D, Mujoo K, Blake ME, Arntzen CJ, Gutterman JU. Avicins: Triterpenoid saponins from Acacis victoriae (Bentham) induce apoptosis by mitochondrial perturbation. Proc Natl Acad Sci USA 2001, 98:5821-5826. 11344312, 10.1073/pnas.101619098, 33297.
12. Asamizu E, Nakamura Y, Sato S, Tabata S. Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus. DNA Res 2000, 7:127-130. 10819328, 10.1093/dnares/7.2.127.
13. Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 2006, 7:272. 17062153, 10.1186/1471-2164-7-272, 1635983.
14. FAOSTAT data 2004. , http://faostat.fao.org
15. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 2005, 5:16. 16107212, 10.1186/1471-2229-5-16, 1215491.
16. Bhushan D, Pandey A, Chattopadhyay A, Choudhary MK. Extracellular Matrix Proteome of Chickpea (Cicer arietinum L.) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect. J Proteome Res 2006, 5:1711-1720. 16823979, 10.1021/pr060116f.
17. Pandey A, Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A, Chakraborty N. The Nuclear Proteome of Chickpea (Cicer arietinum L.) Reveals Predicted and Unexpected Proteins. J Prot Res 2006, 5:3301-3311.
18. Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S, Chakraborty N. Comparative proteomic analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol Cell Prot 2007, 6:1868-1884.
19. Pandey A, Chakraborty S, Datta A, Chakraborty N. Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol Cell Prot 2008, 7:88-107.
20. Leslie JF, Summerell BA. The Fusarium laboratory workshop manual. 2006, Blackwell publishing, USA.
21. Nene YL, Reddy MV, Haware MP, Ghanekar AM, Amin KS. Field diagnosis of chickpea diseases and their control. Information Bulletin 1991, 28. ICRISAT, Patancheru, India.
22. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999, 9:868-877. 10508846, 10.1101/gr.9.9.868, 310812.
23. Zhang S, Klessig DF. MAPK cascades in plant defense signaling. Trend Plant Sci 2001, 6:520-527.
24. Karlova R, Boeren S, Russinova E, Aker J, Vervoort J, De Vries S. The Arabidopsis somatic embryogenesis receptor-like kinase 1 protein complex includes brassinosteroid-insensitive 1. Plant Cell 2006, 3:626-638.
25. Roberts MR, Bowles DJ. Fusicoccin, 14-3-3 proteins, and defense responses in tomato plants. Plant Cell 1999, 119:1243-1250.
26. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM. The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 1998, 10:1307-1319. 9707531, 10.1105/tpc.10.8.1307, 144378.
27. Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S. A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. Plant Cell 2007, 19:2403-2416. 17704213, 10.1105/tpc.107.053579, 2002612.
28. Lee MH, Lee SH, Kim H, Jin JB, Kim DH, Hwang I. A WD40 repeat protein, Arabidopsis Sec13 homolog 1, may play a role in vacuolar trafficking by controlling the membrane association of AtDRP2A. Mol Cells 2006, 22:210-219.
29. Holm M, Hardtke CS, Gaudet R, Deng X-W. Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 2001, 20:118-127. 11226162, 10.1093/emboj/20.1.118, 140188.
30. Kim SH, Hong JK, Lee SC, Sohn KH, Jung HW, Hwang BK. CAZFP1, Cys2/His2-type zinc-finger transcription factor gene functions as a pathogen-induced early-defense gene in Capsicum annuum. Plant Mol Biol 2004, 55:883-904.
31. Thurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K, Gatz C. Tobacco bZIP transcription factor TGA22 and related factor TGA21 have distinct roles in plant defense responses and plant development. Plant J 2005, 44:100-113. 16167899, 10.1111/j.1365-313X.2005.02513.x.
32. Eulgem T. Dissecting the WRKY web of plant defense regulators. PLoS Pathog 2006, 2:e126. 17121464, 10.1371/journal.ppat.0020126, 1657070.
33. Gong Z, Dong CH, Lee H, Zhu J, Xiong L, Gong D, Stevenson B, Zhu JK. A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell 2005, 17:256-267. 15598798, 10.1105/tpc.104.027557, 544503.
34. Futamura N, Ishiiminami N, Hayashida N, Shinohara K. Expression of DnaJ homologs and Hsp70 in the Japanese willow (Salix gilgiana Seemen). Plant Cell Physiol 1999, 40:524-531.
35. Dreher K, Callis J. Ubiquitin, hormones and biotic stress in plants. Annals Bot 2007, 99:787-822.
36. Wang L, Xu YY, Ma QB, Li D, Xu ZH, Chong K. Heterotrimeric G protein alpha subunit is involved in rice brassinosteroid response. Cell Res 2006, 16:916-922. 17117160, 10.1038/sj.cr.7310111.
37. Suharsono U, Fujisawa Y, Kawasaki T, Iwasaki Y, Satoh H, Shimamoto K. The heterotrimeric G protein α susnit acts upstream of the small GTPase Race in disease resistance of rice. Proc Natl Acad Sci USA 2002, 99:13307-13312. 12237405, 10.1073/pnas.192244099, 130629.
38. Laxalt AM, Cassia RO, Sanllorenti PM, Madrid EA, Andreu AB, Daleo GR, Conde RD, Lamattina L. Accumulation of cytosolic glyceraldehyde-3-phosphate dehydrogenase RNA under biological stress conditions and elicitor treatments in potato. Plant Mol Biol 1996, 30:961-972. 8639754, 10.1007/BF00020807.
39. Cushman JC, Meyer G, Michalowski CB, Schmitt JM, Bohnert HJ. Salt stress leads to differential expression of two isogenes of phosphoenolpyruvate carboxylase during Crassulacean acid metabolism induction in the common ice plant. Plant cell 1989, 7:715-725.
40. Di Matteo A, Federici L, Mattei B, Salvi G, Johnson KA, Sauino C, De Lorenzo G, Tsernoglou D, Cervone F. The crystal structure of polygalacturonose-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense. Proc Natl Acad Sci USA 2003, 100:10124-10128. 12904578, 10.1073/pnas.1733690100, 187787.
41. De Lorenzo G, Ferrari S. Polygalacturonase-inhibiting proteins in defense against phytopathogenic fungi. Curr Opin Plant Biol 2002, 5:295-299. 12179962, 10.1016/S1369-5266(02)00271-6.
42. Yamaguchi T, Nakayama K, Hayashi T, Tanaka Y, Koike S. Molecular cloning and characterization of a novel beta-1,3-glucanase gene from rice. Biosci Biotechnol Biochem 2002, 66:1403-1406. 12162569, 10.1271/bbb.66.1403.
43. Real MD, Company P, García-Agustín P, Bennett AB, González-Bosch C. Characterization of tomato endo-beta-1,4-glucanase Cel1 protein in fruit during ripening and after fungal infection. Planta 2004, 220:80-86. 15243740, 10.1007/s00425-004-1321-7.
44. Lee SJ, Suh MC, Kim S, Kwon JK, Kim M, Paek KH, Choi D, Kim BD. Molecular cloning of a novel pathogen-inducible cDNA encoding a putative acyl CoA synthetase from capsicum annum. Plant Mol Biol 2001, 46:661-671. 11575721, 10.1023/A:1011677028605.
45. Knudsen J, Jensen MV, Hansen JK, Faergeman NJ, Neergaard TB, Gaigg B. Role of acylCoA binding protein in acylCoA transport, metabolism and cell signalling. Mol Cell Biochem 1999, 192:95-103. 10331663, 10.1023/A:1006830606060.
46. Liu JH, Nada K, Honda C, Kitashiba H, Wen XP, Pang XM, Moriguchi T. Polyamine biosynthesis of apple callus under salt stress: importance of the arginine decarboxylase pathway in stress response. J Exp Bot 2006, 57:2589-2599. 16825316, 10.1093/jxb/erl018.
47. Akiyama T, Jin S. Molecular cloning and characterization of an arginine decarboxylase gene up-regulated by chilling stress in rice seedlings. J Plant Physiol 2007, 164:645-654. 16769152, 10.1016/j.jplph.2006.04.006.
48. Weltmeier F, Ehlert A, Mayer CS, Dietrich K, Wang X, Schütze K, Alonso R, Harter K, Vicente-Carbajosa J, Dröge-Laser W. Combinatorial control of Arabidopsis proline dehydrogenase transcription by specific heterodimerisation of bZIP transcription factors. EMBO J 2006, 25:3133-3143. 16810321, 10.1038/sj.emboj.7601206, 1500977.
49. Fukamatsu Y, Naoto Y, Hasunuma K. Arabidopsis NDK1 is a component of ROS signaling by interacting with three catalses. Plant Cell Physiol 2003, 44:982-989. 14581623, 10.1093/pcp/pcg140.
50. Nagata T, Iizumi S, Satoh K, Kikuchi S. Comparative molecular biological analysis of membrane transport genes in organisms. Plant Mol Biol 2008, 66:565-585. 18293089, 10.1007/s11103-007-9287-z, 2268718.
51. Kobae Y, Sekino T, Yoshioka H, Nakagawa T, Martinoia E, Maeshima M. Loss of AtPDR8, a plasma membrane ABC transporter of Arabidopsis thaliana, causes hypersensitive cell death upon pathogen infection. Plant Cell Physiol 2006, 47:309-318. 16415066, 10.1093/pcp/pcj001.
52. Simmons CR, Fridlender M, Navarro PA, Yalpani N. A maize defense-inducible gene is a major facilitator superfamily member related to bacterial multidrug resistance efflux antiporters. Plant Mol Biol 2003, 52:433-446. 12856948, 10.1023/A:1023982704901.
53. Pei ZM, Ward JM, Harper JF, Schroeder JI. A novel chloride channel in Vicia faba guard cell vacuoles activated by the serine/threonine kinase, CDPK. EMBO J 1996, 15:6564-6574. 452481, 8978683.
54. Zhang WH, Walker NA, Patrick JW, Tyerman SD. Pulsing Cl-channels in coat cells of developing bean seeds linked to hypo-osmotic turgor regulation. J Exp Bot 2004, 55:993-1001. 15047765, 10.1093/jxb/erh120.
55. Ramsperger-Gleixner M, Geiger D, Hedrich R, Sauer N. Differential expression of sucrose transporter and polyol transporter genes during maturation of common plantain companion cells. Plant Physiol 2004, 134:147-160. 14630956, 10.1104/pp.103.027136, 316295.
56. Bostock RM. Signal crosstalk and induced resistance: Straddling the Line between cost and benefit. Annu Rev Phytopathol 2005, 43:545-580. 16078895, 10.1146/annurev.phyto.41.052002.095505.
57. Potters G, Pasternak TP, Guisez Y, Palme KJ, Jansen MA. Stress-induced morphogenic responses: growing out of trouble?. Trends Plant Sci 2007, 12:98-105. 17287141, 10.1016/j.tplants.2007.01.004.
58. Barth C, Moeder W, Klessig DF, Conklin PL. The timing of senescence and response to pathogens is altered in the ascorbate-deficient Arabidopsis mutant vitamin c-1. Plant Physiol 2004, 134:1784-1792. 15064386, 10.1104/pp.103.032185, 419851.
59. Agizzio AP, Carvalho AO, Ribeiro Sde F, Machado OL, Alves EW, Okorokov LA, Samarão SS, Bloch C, Prates MV, Gomes VM. A 2S albumin-homologous protein from passion fruit seeds inhibits the fungal growth and acidification of the medium by Fusarium oxysporum. Arch Biochem Biophys 2003, 416:188-195. 12893296, 10.1016/S0003-9861(03)00313-8.
60. Grant JJ, Loake GJ. Role of reactive oxygen intermediates and cognate redox signaling in disease resistance. Plant Physiol 2000, 124:21-29. 10982418, 10.1104/pp.124.1.21, 1539275.
61. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F. The reactive oxygen gene network of plants. Trends Plant Sci 2004, 9:490-498. 15465684, 10.1016/j.tplants.2004.08.009.
62. Arnholdt-Schmitt B, Costa JH, de Melo DF. AOX--a functional marker for efficient cell reprogramming under stress?. Trends Plant Sci 2006, 11:281-287. 16713324, 10.1016/j.tplants.2006.05.001.
63. Dixon RA, Achnine L, Kota P, Liu CJ, Reddy MSS, Wang L. The phenylpropanoid pathway and plant defense - a genomics perspective. Mol Plant Pathol 2002, 3:371-390.
64. Zabala G, Zou1 J, Tuteja J, Gonzalez1 DO, Clough SJ, Vodkin LO. Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Plant Biol 2006, 6:26. 17083738, 10.1186/1471-2229-6-26, 1636052.
65. Takahashi H, Hayashi M, Goto F, Sato S, Soga T, Nishioka T, Tomita M, Kawai-Yamada M, Uchimiya H. Evaluation of metabolic interaction in transgenic rice over expressing dihydroflruone-4-reductase. Ann Bot 2006, 98:819-825. 16849376, 10.1093/aob/mcl162.
66. Gowri G, Bugos RC, Campbell WH, Maxwell CA, Dixon RA. Stress responses in Alfalfa (Medicago sativa L): X-molecular cloning and expression of S-adenosyl-I-methionine; Caffeic acid 3-0-methyltransferase, a key enzyme of lignin biosynthesis. Plant Physiol 1991, 97:7-14. 16668418, 10.1104/pp.97.1.7, 1080956.
67. Kader JC. Lipid-transfer proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 1996, 47:627-654. 15012303, 10.1146/annurev.arplant.47.1.627.
68. Ralph SG, Jancsik S, Bohlmann J. Dirigent proteins in conifer defense II Extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). Phytochemistry 2007, 68:1975-1991. 17590394, 10.1016/j.phytochem.2007.04.042.
69. Gidrol X, Sabelli PA, Fern YS, Kush AK. Annexin-like protein from Arabidopsis thaliana rescues delta oxyR mutant of Escherichia coli from H2O2 stress. Proc Natl Acad Sci USA 1996, 93:11268-11273. 8855345, 10.1073/pnas.93.20.11268, 38319.
70. Brkljacic JM, Samardzic JT, Timotijevic GS, Maksimovic VR. Expression analysis of buckwheat (Fagopyrum esculentum Moench) metallothionein-like gene (MT3) under different stress and physiological conditions. J Plant Physiol 2004, 161:741-746. 15266722, 10.1078/0176-1617-01211.
71. Zhu H, Choi H-K, Cook DR, Shoemaker RC. Bridging model and crop legumes through comparative genomics. Plant Physiol 2005, 137:1189-1196. 15824281, 10.1104/pp.104.058891, 1088312.
72. Choi H-K, Mun J-H, Kim D-J, Zhu H, Baek J-M, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR. Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 2004, 43:15289-15294.
73. Wi SJ, Kim WT, Park KY. Overexpression of carnation S-adenosylmethionine decarboxylase gene generates a broad-spectrum tolerance to abiotic stresses in transgenic tobacco plants. Plant Cell Rep 2006, 25:1111-1121. 16642382, 10.1007/s00299-006-0160-3.
74. Vieira Dos Santos C, Cuiné S, Rouhier N, Rey P. The Arabidopsis plastidic methionine sulfoxide reductase B proteins. Sequence and activity characteristics, comparison of the expression with plastidic methionine sulfoxide reductase A, and induction by photooxidative stress. Plant Physiol 2005, 138:909-922. 15923321, 10.1104/pp.105.062430, 1150407.
75. Cona A, Rea G, Angelini R, Federico R, Tavladoraki P. Functions of amine oxidases in plant development and defence. Trends Plant Sci 2006, 11:80-88. 16406305, 10.1016/j.tplants.2005.12.009.
76. Osakabe Y, Maruyama K, Seki M, Satou M, Shinozaki K, Yamaguchi-Shinozaki K. An LRR receptor kinase, RPK1, is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis. Plant Cell 2005, 17:1105-1119. 15772289, 10.1105/tpc.104.027474, 1087989.
77. Suzuki N, Rizhsky L, Liang H, Shuman J, Shulaev V, Mittler R. Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c. Plant Physiol 2005, 139:1313-1322. 16244138, 10.1104/pp.105.070110, 1283768.
78. Kong L, Ohm HW, Anderson JM. Expression analysis of defense-related genes in wheat in response to infection by Fusarium graminearum. Genome 2007, 50:1038-1048. 18059549, 10.1139/G07-085.
79. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS. SNP discovery via 454 transcriptome sequencing. Plant J 2007, 51:910-918. 17662031, 10.1111/j.1365-313X.2007.03193.x, 2169515.
80. Luchhini S, Thompson A, Hinton JCD. Microarrays for microbiologists Microbiology. 2001, 147:1403-1414.
81. de La Chesnaye E, Kerr B, Paredes A, Merchant-Larios H, Méndez JP, Ojeda SR. Fbxw15/Fbxo is an F-Box Protein-Encoding Gene Selectively Expressed in Oocytes of the Murine Ovary. Biol Reprod 2008, 4:714-725.
82. Reddy PH, McWeeney S, Park BS, Manczak M, Gutala RV, Partovi D, Jung Y, Yau V, Searles R, Mori M, Quinn J. Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease. Hum Mol Genet 2004, 13:1225-1240. 15115763, 10.1093/hmg/ddh140.
83. Lu DP, Christopher DA. Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana. Mol Genet Genomics 2008, 280:199-210. 18574595, 10.1007/s00438-008-0356-z.
84. Gray WM. Plant defense: A New Weapon In The Arsenal. Currt Biol 2002, 12:352-354.
85. Vieira Dos Santos C, Rey P. Plant thioredoxins are key actors in the oxidative stress response. Trends Plant Sci 2006, 11:329-34. 16782394, 10.1016/j.tplants.2006.05.005.
86. Lee SH, Ahsan N, Lee KW, Kim DH, Lee DG, Kwak SS, Kwon SY, Kim TH, Lee BH. Simultaneous overexpression of both CuZn superoxide dismutase and ascorbate peroxidase in transgenic tall fescue plants confers increased tolerance to a wide range of abiotic stresses. J Plant Physiol 2007, 164:1626-38. 17360071, 10.1016/j.jplph.2007.01.003.
87. Meyer AJ. The integration of glutathione homeostasis and redox signaling. J Plant Physiol 2008, 165:1390-1403. 18171593, 10.1016/j.jplph.2007.10.015.
88. Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JWS, Shaw PJ. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. MBC 2005, 16:260-269. 15496452, 10.1091/mbc.E04-09-0791, 539170.
89. Yang AH, Yeh KW. Molecular cloning, recombinant gene expression, and antifungal activity of cystatin from taro (Colocasia esculenta cv. Kaosiung no. 1). Planta 2005, 221:493-501. 15647900, 10.1007/s00425-004-1462-8.
90. Devoto A, Muskett PR, Shirasu K. Role of ubiquitination in the regulation of plant defence against pathogens. Curr Opin Plant Biol 2003, 6:307-311. 12873523, 10.1016/S1369-5266(03)00060-8.
91. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana. Science 2007, 317:338-342. 17641193, 10.1126/science.1138632.
92. Tao Y, Xie Z, Chen W, Glazebrook J, Chang H-S, Han B, Zhu T, Zou G, Katagiri F. Quantitative Nature of Arabidopsis Responses during Compatible and Incompatible Interactions with the Bacterial Pathogen Pseudomonas syringae. Plant Cell 2003, 15:317-330. 12566575, 10.1105/tpc.007591, 141204.
93. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997, 7:986-995.
94. Streatfield SJ, Weber A, Kinsman EE, Hausler RE, Ji J, Post-Beittenmillor D, Kaiser WM, Pyke KA, Flugge UI. The phosphoenolyruvate/phosphate palisade cell development and plastid dependant nuclear gene expression. Plant Cell 1999, 11:1609-1621. 10488230, 10.1105/tpc.11.9.1609, 144315.
95. Zhang Y, Wang Y, Jiang L, Xu Y, Wang Y, Lu D, Chen F. Aquaporin JcPIP2 is involved in drought responses in Jatropha curcas. Acta Biochim Biophys Sin 2007, 10:787-794.
96. Reimers PJ, Guo A, Leach JE. Increased Activity of a Cationic Peroxidase Associated with an Incompatible Interaction Between Xanthomonas oryzae pv oryzae and Rice (Oryza sativa). Plant Physiol 1992, 99:1044-1050. 16668969, 10.1104/pp.99.3.1044, 1080582.
97. Sawada K, Hasegawa M, Tokuda L, Kameyama J, Kodama O, Yoshida K, Shinmyo A. Enhanced resistance to blast fungus and bacterial blight in transgenic rice constitutively expressing OsSBP, a rice homologue of mammalian selenium binding proteins. Biosci Biotechnol Biochem 2004, 68:873-880. 15118317, 10.1271/bbb.68.873.
98. Hennig M, Schlesier B, Pfeffer S, Höhne WE. Narbonin, a 2 S globulin from Vicia narbonensis L. Crystallization and preliminary crystallographic data. J Mol Biol 1990, 215:339-40. 2231708, 10.1016/S0022-2836(05)80354-7.
99. Dunwell JM, Purvis A, Khuri S. Cupins: the most functionally diverse protein superfamily?. Phytochemistry 2004, 65:7-17. 14697267, 10.1016/j.phytochem.2003.08.016.
100. Wang D, Pajerowska-Mukhtar K, Culler AH, Dong X. Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol 2007, 17:1784-1790. 17919906, 10.1016/j.cub.2007.09.025.
101. Malatrasi M, Corradi M, Svensson JT, Close TJ, Close TJ, Marmiroli N. A branched-chain amino acid aminotransferase gene isolated from Hordeum vulgare is differentially regulated by drought stress. Theor Appl Genet 2006, 113:965-976. 16932885, 10.1007/s00122-006-0339-6.
102. Wang TW, Zhang CG, Wu W, Nowack LM, Madey E, Thompson JE. Antisense suppression of deoxyhypusine synthase in tomato delays fruit softening and alters growth and development. Plant Physiol 2005, 138:1372-1382. 15951486, 10.1104/pp.105.060194, 1176410.
103. Hirayama T, Oka A. Novel protein kinase of Arabidopsis thaliana (APK1) that phosphorylates tyrosine, serine and threonine. Plant Mol Biol 1992, 20:653-662. 1450380, 10.1007/BF00046450.
104. Reise L, Modrusan Z, Margossian L, Samach A, Ohad N, Haughn GW, Fischer RL. The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell 1995, 83:735-742. 8521490, 10.1016/0092-8674(95)90186-8.
105. Hatton D, Gray JC. Two MAR DNA-binding proteins of the pea nuclear matrix identify a new class of DNA-binding proteins. Plant J 1999, 18:417-429. 10406125, 10.1046/j.1365-313X.1999.00468.x.
106. Yamano Y, Ohyama K, Ohta M, Sano T, Ritani A, Shimada J, Ashida N, Yoshida E, Ikehara K, Morishima I. A novel spermatogenesis related factor-2 (SRF-2) gene expression affected by TCDD treatment. Endocr J 2005, 52:75-81. 15758561, 10.1507/endocrj.52.75.
107. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual. 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
108. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automatedsequencer traces using Phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
109. Graham MA, Silverstein KAT, Cannon SB, VandenBosch KA. Computational identification and characterization of novel genes from legumes. Plant Physiol 2004, 135:1179-1197. 15266052, 10.1104/pp.104.037531, 519039.