Identification and analyses of DNA-binding with One zinc Finger (DOF) transcription factor family in Medicago truncatula

HAL Id: hal-01603780

https://hal.archives-ouvertes.fr/hal-01603780

Submitted on 5 Jun 2020

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License

Identification and analyses of DNA-binding with One zinc Finger (DOF) transcription factor family in

Medicago truncatula

Rana Muhammad Atif, Richard Thompson, Sergio Ochatt

To cite this version:

Rana Muhammad Atif, Richard Thompson, Sergio Ochatt. Identification and analyses of DNA-

binding with One zinc Finger (DOF) transcription factor family in Medicago truncatula. 3. Annual

Computational Science Conference, May 2015, Islamabad, Pakistan. �hal-01603780�

Identification and analyses of DNA-binding with One zinc Finger (DOF) transcription factor family in Medicago truncatula

Rana Muhammad Atif

*, Richard Thampson

, Sergio Ochatt

1

INRA, UMR Agroécologie, pôle GEAPSI, 17 rue Sully, 21000 Dijon, France.

2

Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.

3

Center for Advanced Studies in Food Security-Agriculture, University of Agriculture, Faisalabad, Pakistan.

ABSTRACT

DOF proteins are plant-specific transcription factors which have been implicated in diverse plant processes such as seed germination, seed development, carbohydrate and secondary metabolism, light mediated gene regulation, vascular tissue development, disease response, cell cycle regulation and hormone homeostasis. Owing to their importance in plant genomes, a systematic in-silico analysis was carried out to identify non-redundant genes encoding C2-C2 DOF Zn-finger domain containing transcription factor family in the model legume M. truncatula genome. A total of 22 Dof genes encoding complete DOF domain were predicted and renamed as MtDof (Medicago truncatula Dof). Gene localization studies demonstrated that putative MtDof genes were localized over seven out of eight M. truncatula chromosomes. Exon/intron structure analysis has shown some intron-less Dof genes which might have resulted from intron loss during evolution.

Evolutionary studies suggested that tandem duplications were predominantly responsible for the expansion of the DOF TF family during evolution in M. truncatula. The comparison of DOF DNA- binding domain in all the MtDOF proteins revealed a high level of residue conservation with 31 out of 52 amino acids being 100% conserved in all 22 proteins. A comparative phylogenetic tree of 69 DOF protein (from Arabidopsis, pea and M. truncatula) revealed six distinct groups of DOF proteins. A total of 26 different conserved domains has been identified in 69 DOF proteins, indicating the gene duplication events during the evolutionary process. Some of the groups in phylogenetic tree contain single or double conserved domains, while others contain multiple conserved domains. These computational studies paved the way for better understanding the molecular evolution and functional diversity of DOF TF family in M. truncatula.

Keywords: Model legume, Zinc finger, Gene structure, Phylogenetic tree, Genome evolution,