Genome-wide analysis of the auxin response factor (ARF) gene family in Phaseolus vulgaris

Fatemi, Sohaila; Mirzaei, Khaled; Kamangar, Mohamed Sedigh

Genome-wide analysis of the auxin response factor (ARF) gene family in Phaseolus vulgaris

Document Type : Research Paper

Authors

¹ M.Sc. of Biotechnology in Agriculture, University of Kurdistan, Sanandaj, Iran

² Ph.D. Student, Earth & Life Institute, Biodiversity Research Centre, Université Catholique de Louvain (UCL), B-1348 Belgium

Abstract

Auxin has an important role in the various stages of plants growth and development. Studies have shown that auxin regulates these processes by auxin responsefactors (ARF) family. ARF proteins due to their central domain, mediate the cellular response to the auxin by activating or repressing the expression of downstream genes. ARF genes in several different plant species have been studied by molecular methods however to better understand the mechanisms of these proteins more studies are needed. In this study with computational methods, we found 27 ARF proteins, which they were scattered on the different parts of Phaseolus vulgaris chromosomes. The phylogenetic analysis of these sequences revealed they were divided into four different classes without any sign of gene-duplication between them. ARF genes expression according to the types of gene and based on the types of tissue respectively showed that they group into the five and two classes. In comparing with other tissues, ARF genes in leaf, young trifoliates, stems, mature pods and young pods tissues have a high level of expression. Of the 27 ARF Phaseolus vulgaris sequences surveyed in this study, nine ARF proteins were gene activator and 17 ARF proteins were gene suppressor.

Keywords

20.1001.1.22520783.1396.7.19.4.5

Main Subjects

Bioinformatics

References

Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr. Opin. Plant. Biol. 8: 135-141.

Ariani A, Gepts P (2015) Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.). Mol. Genet. Genomics. 290: 1771-1785.

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic. Acids. Res. 31, no. 13: 3497-3500.

Di DW, Zhang C, Luo P, An CW, Guo GQ (2016) The biosynthesis of auxin: how many paths truly lead to IAA? Plant. Growth. Regul. 78: 275-285.

Ellis CM, Nagpal P, Young JC, Hagen G, Guilfoyle TJ, Reed JW (2005) Auxin response factor1 and Auxin response factor2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development. 132: 4563-4574.

Finet C, Fourquin C, Vinauger M, Berne‐Dedieu A, Chambrier P, Paindavoine S, Scutt CP (2010) Parallel structural evolution of auxin response factors in the angiosperms. Plant. J. 63: 952-959.

Goetz M, Vivian-Smith A, Johnson SD, Koltunow AM (2006) AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis. Plant. Cell. 18: 1873-1886.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2011) Phytozome: a comparative platform for green plant genomics. Nucleic. Acids. Res. 40: 1178-1186.

Guilfoyle TJ (2015) The PB1 domain in auxin response factor and Aux/IAA proteins: a versatile protein interaction module in the auxin response. Plant. Cell. 27: 33-43.

Harper RM, Stowe-Evans EL, Luesse DR, Muto H, Tatematsu K, Watahiki MK, Yamamoto K, Liscum E (2000) The NPH4 locus encodes the auxin response factor ARF7, a conditional regulator of differential growth in aerial Arabidopsis tissue. Plant. Cell. 12:757–770

Hunter C, Willmann MR, Wu G, Yoshikawa M, de la Luz Gutiérrez-Nava M, Poethig SR (2006) Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development. 133: 2973-2981.

Kumar R, Tyagi AK, Sharma AK (2011) Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Mol. Genet. Genomics. 285: 245-260.

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Boil. Evol: msw054.

Li SB, OuYang WZ, Hou XJ, Xie LL, Hu CG, Zhang JZ (2015) Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis). Front. Plant. Sci. 6: 119.

Li SB, Xie ZZ, Hu CG, Zhang JZ (2016) A Review of auxin response factors (ARFs) in plants. Front. Plant. Sci 7.

Liu Y, Jiang H, Chen W, Qian Y, Ma Q, Cheng B, Zhu S (2011) Genome-wide analysis of the auxin response factor (ARF) gene family in maize (Zea mays). Plant. Growth. Regul. 63: 225-234.

López-Pedrouso M, Bernal J, Franco D, Zapata C (2014) Evaluating Two-Dimensional Electrophoresis Profiles of the Protein Phaseolin as Markers of Genetic Differentiation and Seed Protein Quality in Common Bean (Phaseolus vulgaris L.). J. Agric. Food. Chem. 62: 7200-7208.

Mirzaei K, Bahramnejad B, Shamsifard MH, Zamani W (2014) In silico identification, phylogenetic and bioinformatic analysis of argonaute genes in plants. Int. J. Genomics. 2014.

Pandurangan S, Diapari M, Yin F, Munholland S, Perry GE, Chapman BP, Huang S, Sparvoli F, Bollini R, Crosby WL, Pauls KP (2016) Genomic Analysis of Storage Protein Deficiency in Genetically Related Lines of Common Bean (Phaseolus vulgaris). Front. Plant. Sci 7.

Ren XY, Vorst O, Fiers MW, Stiekema WJ, Nap JP (2006) In plants, highly expressed genes are the least compact. Trends. Genet. 22: 528-532.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet 46: 707-713.

Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant. Cell. 15: 533-543.

Van Ha C, Le DT, Nishiyama R, Watanabe Y, Sulieman S, Tran UT, Mochida K, Van Dong N, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2013) The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress. DNA Res: dst027.

Zhang S, Wang S, Xu Y, Yu C, Shen C, Qian Q, Geisler M, Jiang DA, Qi Y (2015) The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3‐5 and OsBRI1. Plant. Cell. Environ. 38: 638-654.

Zouine M, Fu Y, Chateigner-Boutin AL, Mila I, Frasse P, Wang H, Audran C, Roustan JP, Bouzayen M (2014) Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing. PLoS One. 9: e84203.