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Genome-Wide Bioinformatics Analysis of DOF Transcription Factor Gene Family of Asparagus and Its Comparative Phylogenetic Assessment with Arabidopsis

By: Humera Amin, Shumaila Dastgir, Muhammad Shafiq, Muhammad Arshad Javed, Muhammad Saleem Haider

Key Words: DNA binding with One Finger, Asparagus, Plant specific transcription factor, Genome-wide.

Int. J. Biosci. 17(6), 103-123, December 2020.

DOI: http://dx.doi.org/10.12692/ijb/17.6.103-123

Certification: ijb 2020 0093 [Generate Certificate]

Abstract

Asparagus officinalis L has been cultivated and harvested from the wild for thousands of years for medicinal purposes. The family of DOF gene (DNA binding with One Finger) is highly conserved and member of this gene family plays an important role in many regulatory mechanisms in plants including plant growth and development. We identified 7 putative DOF genes through the genome mining of asparagus (A. officinalis L.) and distributed unevenly among 5 chromosomes. The DOF gene family in asparagus was phylogenetically analyzed with Arabidopsis thaliana DOF genes and classified into 5 subfamilies. The exon-intron organization of DOF gene in asparagus showed the presence of intron and AoDOF5 (2intron) contain a maximum no of introns. The DOF gene on chromosome in A.officinalis is observed in 4 chromosomes. Maximum 3 DOF genes were observed on chromosome 8 and a single DOF gene was found on other chromosomes. The segmental gene duplication was predominant over tandem duplication which might be the cause of DOF gene family expansion in A.officinalis. The cis-regulatory element analysis revealed the presence of light-responsive, abscisic acid responsiveness, endosperm-specific, anaerobic induction, root-specific expression, gibberellin-responsive, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analysis of DOF genes of A.officinalis with Arabidopsis revealed several orthologs and paralogs assisting in understanding the putative functions of AoDOF genes. The bioinformatics-based genome-wide assessment of DOF gene family of A.officinalis   attempted in the present study could be a significant step for deciphering novel DOF genes based on genome-wide expression profiling.

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Genome-Wide Bioinformatics Analysis of DOF Transcription Factor Gene Family of Asparagus and Its Comparative Phylogenetic Assessment with Arabidopsis

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Humera Amin, Shumaila Dastgir, Muhammad Shafiq, Muhammad Arshad Javed, Muhammad Saleem Haider.
Genome-Wide Bioinformatics Analysis of DOF Transcription Factor Gene Family of Asparagus and Its Comparative Phylogenetic Assessment with Arabidopsis.
Int. J. Biosci. 17(6), 103-123, December 2020.
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