Comprehensive Analyses of NAC Transcription Factor Family in Almond (Prunus dulcis) and Their Differential Gene Expression during Fruit Development.

Zeeshan Zafar,Muhammad Faraz Bhatti,Sidra Fatima

doi:10.3390/plants10102200

Zeeshan Zafar, Muhammad Faraz Bhatti + Show 1 more

Open Access

https://doi.org/10.3390/plants10102200

Copy DOI

Abstract

As plant specific transcription factors, NAC (NAM, ATAF1/2, CUC2) domain is involved in the plant development and stress responses. Due to the vitality of NAC gene family, BLASTp was performed to identify NAC genes in almond (Prunus dulcis). Further, phylogenetic and syntenic analyses were performed to determine the homology and evolutionary relationship. Gene duplication, gene structure, motif, subcellular localization, and cis-regulatory analyses were performed to assess the function of PdNAC. Whereas RNA-seq analysis was performed to determine the differential expression of PdNAC in fruits at various developmental stages. We identified 106 NAC genes in P. dulcis genome and were renamed according to their chromosomal distribution. Phylogenetic analysis in both P. dulcis and Arabidopsis thaliana revealed the presence of 14 subfamilies. Motif and gene structure followed a pattern according to the PdNAC position in phylogenetic subfamilies. Majority of NAC are localized in the nucleus and have ABA-responsive elements in the upstream region of PdNAC. Differential gene expression analyses revealed one and six PdNAC that were up and down-regulated, respectively, at all development stages. This study provides insights into the structure and function of PdNAC along with their role in the fruit development to enhance an understanding of NAC in P. dulcis.

Highlights

Transcription factors have immense importance due to their role in controlling the transcription rate by binding to the cis-regulatory promoter elements [1]
Identified genes were renamed from PdNAC1 to PdNAC106 according to their chromosomal position starting from chromosome 1
Using bioinformatics and phylogenetic analysis, we identified 106 NAC genes in P. dulcis

Summary

Introduction

Transcription factors have immense importance due to their role in controlling the transcription rate by binding to the cis-regulatory promoter elements [1]. DNA binding domain of transcription factors determines their function in gene expression regulatory networks. Transcription factors bind to the cis-regulatory elements resulting in the regulation of the targeted gene for enhance or reduced expression level. Transcription factors are divided into several categories based on the DNA binding domain. These families are bZIP, NAC, MYB, DREB, WRKY, AP2/EREBP, C2H2, and others [2]. Plant’s growth and development depend on the action of these transcription factors in various ways such as hormone signaling, secondary metabolism, organ formation and response to the environment [3,4]. Numerous plant transcription factors are responsible for the improvement of plant tolerance against the abiotic stresses [5]

Objectives

Methods

Results

Discussion

Conclusion