E-ISSN 2756-4843 | ISSN 0794-5698
 

Research Article 


In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species

A. M. Gumi, B. Kumar, A. Pareek, and S. L. Singla-Pareek.

Abstract
The dehydration-responsive element-binding (DREB) genes are types of plant-specific transcription factors that bind to DRE/CRT elements in response to abiotic stresses. It belongs to the AP2 superfamily and contains highly conserved APETELA2 (AP2) domain. In this study, comparative analysis of DREB2A gene from diploid Oryza species was performed using BLASTN approach. The OglDREB2A sequence (KU159742.1) was used as query against 11 diploid Oryza species in the Gramene database for identification of DREB2A orthologs. Molecular characterization, subcellular localization, conserved motifs and promoter analysis were also performed using bioinformatics tools. Molecular characterization of DREB2A protein in the diploid Oryza showed an AP2 conserved domain and nuclear localized protein which is similar to putative transcription factor involved in
stress responses. Motif analysis using MEME suites identified 7 significant motifs across all the diploid Oryza species with motif 2, 3, 4 and 5 as the common motifs with ~50 amino acids length. Analysis of 1kb upstream of TSS of DREB2A of the 11 diploid Oryza species revealed many CAREs associated with stress (DRE, LTRE, ERE, G-box, TCC-motif and Sp1) and hormonal regulations (ABREs, MeJA, GARE, and GC-motif) with ABRE as the common element in all the diploid species. Additionally, wild species has more number of cis elements than the cultivated species suggesting a possible role in genome evolution. Overall, the 11 DREB2A orthologs are conserved in terms of sequence homology and protein structure but cultivated species has less number of transcripts than their progenitors suggesting gene retrogression in cultivated Oryza species.

Key words: In silico Analysis, DREB2A, Rice, Gene retrogression, Transcription factor


 
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How to Cite this Article
Pubmed Style

Gumi AM, Kumar B, Pareek A, Singla-Pareek aSL. In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nig. J. Basic Appl. Sci.. 2022; 30(2): 22-34. doi:10.4314/njbas.v30i2.4


Web Style

Gumi AM, Kumar B, Pareek A, Singla-Pareek aSL. In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. https://www.njbas-udus.com/?mno=46839 [Access: September 14, 2023]. doi:10.4314/njbas.v30i2.4


AMA (American Medical Association) Style

Gumi AM, Kumar B, Pareek A, Singla-Pareek aSL. In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nig. J. Basic Appl. Sci.. 2022; 30(2): 22-34. doi:10.4314/njbas.v30i2.4



Vancouver/ICMJE Style

Gumi AM, Kumar B, Pareek A, Singla-Pareek aSL. In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nig. J. Basic Appl. Sci.. (2022), [cited September 14, 2023]; 30(2): 22-34. doi:10.4314/njbas.v30i2.4



Harvard Style

Gumi, A. M., Kumar, . B., Pareek, . A. & Singla-Pareek, . a. S. L. (2022) In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nig. J. Basic Appl. Sci., 30 (2), 22-34. doi:10.4314/njbas.v30i2.4



Turabian Style

Gumi, A. M., B. Kumar, A. Pareek, and and S. L. Singla-Pareek. 2022. In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nigerian Journal of Basic and Applied Sciences, 30 (2), 22-34. doi:10.4314/njbas.v30i2.4



Chicago Style

Gumi, A. M., B. Kumar, A. Pareek, and and S. L. Singla-Pareek. "In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species." Nigerian Journal of Basic and Applied Sciences 30 (2022), 22-34. doi:10.4314/njbas.v30i2.4



MLA (The Modern Language Association) Style

Gumi, A. M., B. Kumar, A. Pareek, and and S. L. Singla-Pareek. "In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species." Nigerian Journal of Basic and Applied Sciences 30.2 (2022), 22-34. Print. doi:10.4314/njbas.v30i2.4



APA (American Psychological Association) Style

Gumi, A. M., Kumar, . B., Pareek, . A. & Singla-Pareek, . a. S. L. (2022) In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species. Nigerian Journal of Basic and Applied Sciences, 30 (2), 22-34. doi:10.4314/njbas.v30i2.4





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