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. 2021 Oct 16;10(10):2200.
doi: 10.3390/plants10102200.

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

Zeeshan Zafar  1 , Sidra Fatima  1 , Muhammad Faraz Bhatti  1
Affiliations

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

Zeeshan Zafar et al. Plants (Basel). .

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.

Keywords: NAC; RNA-seq; differential gene expression; gene duplication; genome wide identification; phylogenetic analysis; syntenic analysis; transcription factor.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Chromosomal mapping of PdNAC genes. PdNAC genes have been predicted on the chromosomes of P. dulcis. Chromosome numbers is present below each chromosome.
Figure 2
Figure 2
Prediction of cis-regulatory elements of PdNAC. Cis-regulatory elements are shown in upstream region of the PdNAC. Cis-regulatory elements are shown in different colors.
Figure 3
Figure 3
Phylogenetic analysis of P. dulcis and A. thaliana NAC. PdNAC and AtNAC are divided into fourteen subgroups according to the subgrouping of A. thaliana.
Figure 4
Figure 4
Gene structure and motif analysis of PdNAC. (A) Phylogenetic tree, (B) motif pattern, and (C) domain presence. Gene structure shows the presence of introns and exons in the genes.
Figure 5
Figure 5
Gene structure prediction of PdNAC genes: Gene structure of PdNAC genes is shown in the figure where CDS, UTRs and intronic regions of the genes are represented.
Figure 6
Figure 6
Gene duplication in PdNAC. In all, 12 pairs of the genes were duplicated in the PdNAC genes. These genes were located on different chromosomes. Chromosome 8 had no duplicated gene whereas all other contain duplicated genes.
Figure 7
Figure 7
Visualization of the syntenic analysis. Synteny of the P. dulcis NAC has been visualized with the NAC of A. thaliana (A), P. persica (B), J. regia (C), M. domestica (D), and V. vinifera (E). Red lines between the genomes show the synteny between the genes.
Figure 8
Figure 8
Venn diagram of syntenic analysis. The diagram shows the unique and common PdNAC having synteny with A. thaliana, P. persica, J. regia, V. vinifera and M. domestica.
Figure 9
Figure 9
Subcellular localization prediction of PdNAC. Subcellular localization of the PdNAC is shown along with the phylogenetic tree of PdNAC. Majority of the PdNAC are localized in the nucleus.
Figure 10
Figure 10
Differential gene expression. Heatmaps of differential gene expression of PdNAC in almond fruit is shown at developmental stage D12 (A), D17 (B), D22 (C), D27 (D), D32 (E), and D37 (F). Heatmaps are based on Z-score.
See this image and copyright information in PMC

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