Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.)

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Lata, Charu ^a,b   Mishra, Awdhesh Kumar ^c   Muthamilarasan, Mehanathan ^c   Bonthala, Venkata Suresh ^c   Khan, Yusuf ^c   Prasad, Manoj ^c  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b CSIR NATIONAL BOTANICAL RESEARCH INSTITUTE   (India)

^c NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

APETALA2 PROTEIN; ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR; PHYTOHORMONE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; AP2 GENE; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; DROUGHT; ERF GENE; FOXTAIL MILLET; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PLANT GENOME; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SALT STRESS; TANDEM REPEAT; UPREGULATION; ADAPTATION; CHROMOSOME MAP; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; PLANT CHROMOSOME; PROCEDURES; SETARIA (PLANT);

SETARIA ITALICA;

ADAPTATION, PHYSIOLOGICAL; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; MULTIGENE FAMILY; PHYLOGENY; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA; SETARIA PLANT; TRANSCRIPTION FACTORS;

EID: 84912014332     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113092     Document Type: Article

References (73)

1. Muthamilarasan M, Prasad M (2014) Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theor Appl Genet DOI:10.1007/s00122-014-2399-3.
2. Lata C, Gupta S, Prasad M (2013) Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses, Crit Rev Biotechnol 33: 328-343.
3. Zhang G, Liu X, Quan Z, Cheng S, Xu X, et al. (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnol 30: 549-554.
4. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, et al. (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnol 30: 555-561.
5. Lata C, Prasad M (2013) Setaria genome sequencing: An overview. J Plant Biochem Biotechnol 22: 257-260.
6. Muthamilarasan M, Theriappan P, Prasad M (2013) Recent advances in crop genomics for ensuring food security. Curr Sci 105: 155-158.
7. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, et al. (2002) DNAbinding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression, Biochem Biophys Res Commun. 290: 998-1009.
8. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140: 411-432.
9. Jofuku KD, Boer BGW, Montagu MV, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6: 1211-25.
10. Lata C, Yadav A, Prasad M (2011) Role of plant transcription factors in abiotic stress tolerance. In: Shanker A. and Venkateshwarulu B. (eds) Abiotic Stress Response in Plants, INTECH Open Access Publishers, 269-296.
11. Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) AP2/ERF family transcription factors in plant abiotic stress responses. Biochimica et Biophysica Acta 1819: 86-96.
12. Magnani E, Sjölander K, Hake S (2004) From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants, Plant Cell 16: 2265-2277.
13. Shigyo M, Hasebe M, Ito M (2006) Molecular evolution of the AP2 subfamily, Gene 366: 256-265.
14. Saleh A, Pagés M (2003) Plant AP2/ERF transcription factors. Genetika 35: 37-50.
15. Shigyo M, Ito M (2004) Analysis of gymnosperm two-AP2-domain-containing genes. Development Genes Evoln 214: 105-14.
16. Lata C, Prasad M (2011) Role of DREBs in regulation of abiotic stress responses in plants. J Exp Bot 62: 4731-4748.
17. Riechmann JL, Meyerowitz EM (1998) The AP2/EREBP family of plant transcription factors. Biol Chem, 379: 633-646.
18. Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, et al. (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochemical Biophysical Res Comm 371: 468-474.
19. Gil-Humanes J, Piston F, Martin A, Barro F (2009) Comparative genomic analysis and expression of the APETALA2-like genes from barley, wheat, and barley-wheat amphiploids. BMC Plant Biol 9: 66.
20. Dietz KJ, Vogel MO, Viehhauser A (2010) AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling. Protoplasma 245: 3-14.
21. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, et al. (2010) Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera . BMC Genomics 11: 719.
22. Zhuang J, Chen J-M, Yao Q-H, Xiong F, Sun C-C, et al. (2011) Discovery and expression profile analysis of AP2/ERF family genes from Triticum aestivum. Mol Biol Rep 38: 745-753.
23. Zhuang J, Yao Q-H, Xiong A-S, Zhang J (2011) Isolation, Phylogeny and Expression Patterns of AP2-Like Genes in Apple (Malus 6 domestica Borkh). Plant Mol Biol Rep 29: 209-216.
24. Zhang G, Chen M, Chen X, Xu Z, Guan S, et al. (2008) Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.). J Exp Bot 59: 4095-4107.
25. Xu W, Li F, Ling L, Liu A (2013) Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.). BMC Genomics 14: 785.
26. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301.
27. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
28. Lee TH, Tang H, Wang X, Paterson AH (2012) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41: D1152-D1158.
29. Tang H, Bowers JE, Wang X, Ming R, Alam M, et al. (2008) Synteny and Collinearity in Plant Genomes, Science 320: 486-488.
30. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
31. Shiu S-H, Bleecker AB (2003) Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis. Plant Physiol 132: 530-543.
32. Du D, Zhang Q, Cheng T, Pan H, Yang W, et al. (2012) Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume . Mol Biol Rep 40: 1937-1946.
33. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29: 1023-1026.
34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
35. Conesa A, Gotz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008: 619832.
36. Khan Y, Yadav A, Suresh BV, Muthamilarasan M, Yadav CB, et al. (2014) Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database. Plant Cell Tiss Organ Cult 118: 279-292.
37. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612.
38. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
39. Yang Z, Gu S, Wang X, Li W, Tang Z, et al. (2008) Molecular evolution of the cpp-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67: 266-277.
40. Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, et al. (2013) Facing growth in the European Nucleotide Archive. Nucleic Acids Res 41: D30-D35.
41. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, et al. (2006) TM4 microarray software suite. Methods Enzymol 411: 134-193.
42. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, opensource system for microarray data management and analysis. Biotechniques 34: 374-378.
43. Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophys Res Commun 393: 720-727.
44. Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of a SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62: 3387-3401.
45. Kumar K, Muthamilarasan M, Prasad M (2013) Reference genes for quantitative Real-time PCR analysis in the model plant foxtail millet (Setaria italica L.) subjected to abiotic stress conditions. Plant Cell Tiss Organ Cult 115: 13-22.
46. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using realtime quantitative PCR and the 2 2DDCt method. Methods 25: 402-408.
47. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, et al. (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20: 197-207.
48. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, et al. (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE 8: e67742.
49. Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, et al. (2014) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21: 41-52.
50. Suresh BV, Muthamilarasan M, Misra G, Prasad M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS ONE 8: e71418.
51. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235-242.
52. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4: 363-371.
53. Zhuang J, Peng R-H, Cheng Z-M, Zhang J, Cai B, et al. (2009) Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera. Scientia Horticul. 123: 73-81.
54. Rashid M, Guangyuan H, Guangxiao Y, Hussain J, Xu Y (2012) AP2/ERF transcription factor in rice: genome-wide canvas and syntenic relationships between monocots and eudicots. Evol Bioinform Online 8: 321-355.
55. Bonthala VS, Muthamilarasan M, Roy R, Prasad M (2014) FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets. Mol Biol Rep 41: 6343-6348.
56. Yadav CB, Muthamilarasan M, Pandey G, Prasad M (2014) Identification, characterization and expression profiling of Dicer-like, Argonaute and RNAdependent RNA polymerase gene families in foxtail millet. Plant Mol Biol Rep DOI:10.1007/s11105-014-0736-y.
57. Muthamilarasan M, Bonthala VS, Mishra AK, Khandelwal R, Khan Y, et al. (2014) C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. Funct Integr Genomics 14: 531-543.
58. Muthamilarasan M, Khandelwal R, Yadav CB (2014) Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.). PLOS ONE 9: e109920.
59. Karniely S, Pines O (2005) Single translation-dual destination: mechanisms of dual protein targeting in eukaryotes. Embo Reports 6: 420-425.
60. Song X, Li Y, Hou X (2013) Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 14: 573.
61. Sun Z-M, Zhou M-L, Xiao X-G, Tang Y-X, Wu Y-M (2014) Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance. Funct Integr Genomics 14: 453-466.
62. Chen J, Xia X, Yin W (2009) Expression profiling and functional characterization of a DREB2-type gene from Populus euphratica. Biochem Biophys Res Commun 378: 483-487.
63. Le DT, Nishiyama R, Watanabe Y, Vankova R, Tanaka M, et al. (2012) Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels. PLoS ONE 7(8): e42411.
64. Fang YJ, You J, Xie KB, Xie WB, Xiong LZ (2008) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280: 547-563.
65. Aida M, Beis D, Heidstra R, Willemsen V, Blilou I, et al. (2004) The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119: 109-120.
66. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana . BMC Plant Biol 4: 10.
67. Puranik S, Sahu PP, Mandal SN, B VS, Parida SK, et al. (2013) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8: e64594.
68. Mishra AK, Muthamilarasan M, Khan Y, Parida SK, Prasad M (2014) Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.) PLoS ONE 9: e86852.
69. Zeller G, Henz SR, Widmer CK, Sachsenberg T, Ratsch G, et al. (2009) Stress induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays. Plant J 58: 1068-1082.
70. Lopez CG, Banowetz GM, Peterson CJ, Kronstad WE (2003) Dehydrin expression and drought tolerance in seven wheat cultivars. Crop Science 43: 577-582.
71. Lata C, Prasad M (2014) Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL. J Plant Biochem Biotechnol 23: 119-122.
72. Okamuro JK, Caster B, Villarroel R, van Montagu M, Jofuku KD (1997) The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc Natl Acad Sci USA 94: 7076-7081.
73. Wolfe SA, Nekludova L, Pabo CO (2000) DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct 29: 183-212.