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. 2024 Mar 31;14(1):7610.
doi: 10.1038/s41598-024-57376-5.

Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress

Amaal Maghraby  1 , Mohamed Alzalaty  2
Affiliations

Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress

Amaal Maghraby et al. Sci Rep. .

Abstract

AP2 (APETALA2)/EREBP (ethylene-responsive element-binding protein), cytochrome c oxidase (COX) and nonspecific lipid transfer proteins (LTP) play important roles in the response to drought stress. This is the first study to identify the COX gene in Zea mays L. via genome-wide analysis. The qRT‒PCR results indicated that AP2/EREBP, COX and LTP were downregulated, with fold changes of 0.84, 0.53 and 0.31, respectively, after 12 h of drought stress. Genome-wide analysis identified 78 AP2/EREBP, 6 COX and 10 LTP genes in Z. mays L. Domain analysis confirmed the presence of the AP2 domain, Cyt_c_Oxidase_Vb domain and nsLTP1 in the AP2/EREBP, COX and LTP proteins, respectively. The AP2/EREBP protein family (AP2) includes five different domain types: the AP2/ERF domain, the EREBP-like factor (EREBP), the ethylene responsive factor (ERF), the dehydration responsive element binding protein (DREB) and the SHN SHINE. Synteny analysis of the AP2/EREBP, COX and LTP genes revealed collinearity orthologous relationships in O. sativa, H. vulgare and A. thaliana. AP2/EREBP genes were found on the 10 chromosomes of Z. mays L. COX genes were found on chromosomes 1, 3, 4, 5, 7 and 8. LTP genes were found on chromosomes 1, 3, 6, 8, 9 and 10. In the present study, the Ka/Ks ratios of the AP2/EREBP paralogous pairs indicated that the AP2/EREBP genes were influenced primarily by purifying selection, which indicated that the AP2/EREBP genes received strong environmental pressure during evolution. The Ka/Ks ratios of the COX-3/COX-4 paralogous pairs indicate that the COX-3/COX-4 genes were influenced primarily by Darwinian selection (driving change). For the LTP genes, the Ka/Ks ratios of the LTP-1/LTP-10, LTP-5/LTP-3 and LTP-4/LTP-8 paralogous pairs indicate that these genes were influenced primarily by purifying selection, while the Ka/Ks ratios of the LTP-2/LTP-6 paralogous pairs indicate that these genes were influenced primarily by Darwinian selection. The duplication time of the AP2/EREBP paralogous gene pairs in Z. mays L. ranged from approximately 9.364 to 100.935 Mya. The duplication time of the COX-3/COX-4 paralogous gene pair was approximately 5.217 Mya. The duplication time of the LTP paralogous gene pairs ranged from approximately 19.064 to 96.477 Mya. The major focus of research is to identify the genes that are responsible for drought stress tolerance to improve maize for drought stress tolerance. The results of the present study will improve the understanding of the functions of the AP2/EREBP, COX and LTP genes in response to drought stress.

Keywords: AP2/EREBP; COX; LTP; Drought stress; Evolutionary analysis; Genome-wide identification.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Sequence identity of the AP2/EREBP, COX and LTP proteins.
Figure 2
Figure 2
Maximum likelihood phylogenetic tree of the AP2/EREBP protein family in Z. mays L.; the proteins are labeled with ☆ for the AP2/ERF domain, ○ for the EREBP-like factor (EREBP), □ for the ethylene responsive factor (ERF), ◇ for the dehydration responsive element binding protein (DREB) and ◁ for the SHN SHINE.
Figure 3
Figure 3
Distribution of the AP2/EREBP, COX and LTP genes on Z. mays L. chromosomes.
Figure 4
Figure 4
Segmental and tandem duplication of AP2/EREBP, COX and LTP among the Z. mays L. chromosomes.
Figure 5
Figure 5
The collinear relationships of the AP2/EREBP, COX and LTP genes are shown as colored lines in the phylogenetic tree.
Figure 6
Figure 6
AP2/EREBP proteins. (a) Rectangular phylogenetic tree. (b) Conserved motifs were predicted using MEME. (c) Protein domains. (d) Gene structure.
Figure 7
Figure 7
Cis‐acting elements in the promoter regions (1500 bp upstream of the start codon) of the AP2/EREBP, COX and LTP genes.
Figure 8
Figure 8
Structural analysis of the AP2-EREBP-24, AP2-EREBP-51, AP2-EREBP-53, COX-1, COX-2, COX-5, LTP-1, LTP-3 and LTP-7 proteins.
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