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Identification and characterization of abiotic stress responsive genes in Ricinus communis L. using bioinformatics tools

By: Wajia Noor, Bibi Sadia, Iftikhar Ahmad Baloch, Asyia, Junaid Ahmad, Bibi Safia, Farida

Key Words: Bioinformatics, Arabidopsis thaliana, Salt and cold stress, Homology.

Int. J. Biosci. 16(5), 23-34, May 2020.

DOI: http://dx.doi.org/10.12692/ijb/16.5.23-34

Certification: ijb 2020 0001 [Generate Certificate]

Abstract

Bioinformatics is one of the leading fields in biology for genomics research. In the present research bioinformatics analysis of abiotic stress responsive genes investigation was carried out in Ricinus communis L. Selected twenty-seven genes of model plant Arabidopsis thaliana were searched in Ricinus communis L. The investigated genes belonged from salt, heat, cold and drought stress. Genes were find out using insilico analysis. Homology search was applied using a best available tool of NCBI called BLAST. Homology search gave best results up to 97% query coverage (ANAH-like) for the presence of selected model plant genes in Ricinus communis L. The query coverage results varied from 2% to 97%. Seven genes ANAH (97%), CSD1 (93%), TAF1 (82%), SOS4 (70%), HOS10 (61%) and MPK3 (61%) expressed high query coverage in R. communis L. Ten genes HVA22 (59%), SOS2 (49%), MYBR1 (45%), HOS31 (49%), STZ (42%), DDF1 (41%), BO1 (41%), LOS4 (39%), CDPK1 (37%) and KIN11 (35%) were somewhat similar. While remaining genes expressed similarity less than 30%. Besides query coverage the investigation of conserved domains showed that these predicted genes exhibited conserved domains similar to that of model plant genes. Phylogenetic analysis of some selected genes confirm the genes existence and gave evolutionary aspect of the gene. The identification of abiotic stress responsive genes makes good contribution to the research on this plant and will help to understand the mechanism to respond the stress in this plant.

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Identification and characterization of abiotic stress responsive genes in Ricinus communis L. using bioinformatics tools

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3), 403-410.

Anderson MD, Prasad TK, Martin BA, Stewart CR. 1994. Differential gene expression in chilling-acclimated maize seedlings and evidence for the involvement of abscisic acid in chilling tolerance. Plant Physiology 105(1), 331-339.

Atkinson NJ, Urwin PE. 2012. The interaction of plant biotic and abiotic stresses: from genes to the field. Journal of Experimental Botany 63(10), 35233543.

Chapin FS. 1991. Integrated responses of plants to stress. BioScience, 41(1), 2936.national Journal of Pharmacy and Pharmaceutical Sciences 4(4), 25-29.

Evans WC. 2009. Trease and Evans’ Pharmacognosy E-Book. Elsevier Health Sciences.

Foyer CH, Noctor G. 2005. Redox homeostasis and antioxidant signaling: a metabolic interface between stress perception and physiological responses. The Plant Cell 17(7), 1866-1875.

Ghebremariam KM, Yan L, Zhang Z, Wang Q. 2013. Effect of drought stress on physiological growth parameters of tomato inbred lines at germination stage. European Scientific Journal 9(33),

Han Y, Zheng QS, Wei YP, Chen J, Liu R, Wan HJ. 2015. In silico identification and analysis of phytoene synthase genes in plants. Genetics and Molecular Research 14(3), 9412-9422.

Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Krishnamurthy L. 2011. Large‐scale transcriptome analysis in chickpea (Cicer arietinum L.) an orphan legume crop of the semi‐arid tropics of Asia and Africa. Plant Biotechnology Journal 9(8), 922-931.

Jena J, Gupta AK. 2012. Ricinus communis L. a phytopharmacological review. International Journal of Pharmacy and Pharmaceutical Sciences 4(4), 25-29.

Knight H, Knight MR. 2001. Abiotic stress signalling pathways: specificity and cross-talk. Trends in Plant Science 6(6), 262-267.

Rhee SY, Dickerson J, Xu D. 2006. Bioinformatics and its applications in plant biology. Annual Review for Plant Biology 57(2), 335-360.

Rizhsky L, Liang H, Mittler R. 2002. The combined effect of drought stress and heat shock on gene expression in tobacco. Plant physiology 130(3), 11431151.

Rossi DL, Vicari AP, Franz BK, McClanahan TK, Zlotnik A. 1997. Identification through bioinformatics of two new macrophage proinflammatory human chemokines: MIP-3alpha and MIP-3beta. The Journal of Immunology 158(3), 1033-1036.

Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi SK, Carninci P, Shinozaki K. 2001. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. The Plant Cell

13(1), 61-72.

Shahid MN, Jamal A, Rashid B, Aftab B, Husnain T. 2012. Identification and isolation of salt-stress-responsive transcripts from Gossypium arboreum L. Turkish Journal of Biology 36(6), 746-756.

Sun W, Van MM, Verbruggen N. 2002. Small heat shock proteins and stress tolerance in plants. Biochimica Biophysica Acta (BBA)-Gene Structure and Expression 1577(1), 1-9.

Teige M, Scheikl E, Eulgem T, Dóczi R, Ichimura K, Shinozaki K, Hirt H. 2004. The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Molecular cell 15(1), 141-152.

Wang W, Vinocur B, Shoseyov O, Altman A. 2004. Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in plant science 9(5), 244-252.

Yamaguchi SK, Shinozaki K. 1994. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. The Plant Cell 6(2), 251-264.

Yan S, Tang Z, Su W, Sun W. 2005. Proteomic analysis of salt stress responsive proteins in rice root. Proteomics 5(1), 235-244.

Yokota A, Kawasaki S, Iwano M, Nakamura C, Miyake C, Akashi K. 2002. Citrulline and DRIP‐1 protein (ArgE homologue) in drought tolerance of wild watermelon. Annals of Botany 89(7), 825-832.

Wajia Noor, Bibi Sadia, Iftikhar Ahmad Baloch, Asyia, Junaid Ahmad, Bibi Safia, Farida.
Identification and characterization of abiotic stress responsive genes in Ricinus communis L. using bioinformatics tools.
Int. J. Biosci. 16(5), 23-34, May 2020.
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