Genome-Wide Identification, Structural Characterization and Phylogenetic Analysis of Dof (DNA-Binding with one finger) Transcription Factor in Lima Bean (Phaseolus lunatus L.)

Arif Ullah; Zamarud Shah; Raham Sher Khan; Osaid Kamran Marwat; Kaleem Ullah

Genome-Wide Identification, Structural Characterization and Phylogenetic Analysis of Dof (DNA-Binding with one finger) Transcription Factor in Lima Bean (Phaseolus lunatus L.)

Authors

Arif Ullah PhD Student, Department of Biotechnology, University of Science and Technology Bannu, Pakistan
Zamarud Shah Assistant Professor, Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan,
Raham Sher Khan Professor, Department of Biotechnology, Abdul Wali Khan University Mardan, Pakistan,
Osaid Kamran Marwat M. Phil Student, School of Interdisciplinary Engineering and Sciences, National University of Science and Technology, Islamabad, Pakistan
Kaleem Ullah BS Student, Department of Biotechnology, Abdul Wali Khan University Mardan, Pakistan

Keywords:

Lima bean, Dof, genome-wide analysis, evolutionary analysis, transcription factor

Abstract

Dofs are plant-specific transcription factors involved in diverse functions, including growth, development, hormonal and Abiotic stress response regulation. Although genome-wide analysis of Dof genes has been performed in many species, these genes have yet to be analyzed in lima bean. The current study was aimed at exploring and characterizing the Dof gene family across the genome of the lima bean. Forty PlDof genes in the genome of lima bean were detected during the present study, and named as PlDof1-PlDof40 based on their location on the chromosome in the ascending order. PlDof12 was recorded as the largest gene with 1560 bp CDS, 519 amino acid protein length (PL) and 57.126 kDa protein molecular weight (PMW), while PlDof-23 was found as the smallest one with only 522 CDS, 173 PI and 19.75 kDa PMW, respectively. Nucleus was predicted as a major residence for all 40 PlDof proteins. Isoelectric points and GRAVY were found in the range of 5.35 to 8.91 and -0.269 to -0.746, respectively. The varying number of exons reveals that deletions/additions have occurred during evolution, resulting in variation in motif number. Motif1was conserved in all PlDof genes. The phylogenetic tree reveals that paralogs contributed 33% to the PlDof gene family expansion. Ka/Ks ratios of paralogs reveal that they were all under purifying selection. The promoter region has environmental, developmental, light and hormone-responsive elements that might contribute to the diverse function of PlDof. This study provides a basis for the functional validity of PlDof genes.

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Genome-Wide Identification, Structural Characterization and Phylogenetic Analysis of Dof (DNA-Binding with one finger) Transcription Factor in Lima Bean (Phaseolus lunatus L.)