Genome-Wide Identification and Expression Analysis of Aspartic proteases in Populus euphratica Reveals Candidates Involved in Salt Tolerance

Abstract

Aspartic proteases (APs) are among the four primary families of proteolytic enzymes found in plants, and they are essential for both stress response mechanisms and developmental activities. While the AP gene family has been studied in model plants like Arabidopsis, its characterization in woody species-particularly in extremophytes like Populus euphratica, remains limited. Moreover, the potential involvement of APs in salt tolerance mechanisms in trees is yet to be explored. In this research, 55 PeAPs were discovered and categorized into three distinct classes based on their conserved protein structures. The phylogenetic analysis revealed potential functions of AP genes derived from Arabidopsis thaliana, V. vinifera, and P. euphratica. Our findings indicate that PeAP possesses a well-conserved evolutionary background and contains numerous highly variable regions, making it an excellent candidate for the identification and systematic examination of woody trees. Additionally, motifs frequently found in aspartic proteases within the genome of P. euphratica may be linked to functional PeAPs. It appears that PeAPs are associated with specific gene functions. These genes are influenced by cis-elements, which may play a role in their responsiveness to phytohormone, stress adaptation maybe changed to these genes are regulated by cis-elements that may mediate their responsiveness to phytohormones, abiotic stress, and developmental cues. Our research offers the initial comprehensive analysis of the AP family in P. euphratica, emphasizing its potential functions in adapting to salt conditions. The findings uncover candidate PeAPs for genetic engineering to enhance salinity tolerance in woody crops.

Keywords: Aspartic proteases; Populus euphratica; gene family; salinity tolerance.

Figure 1

Phylogenetic tree, conserved domain analysis of aspartic proteases gene family in Populus euphratica. Individual conserved domains are indicated by different colored boxes.

Figure 2

Phylogenetic tree of aspartic proteases in A. thaliana, Vitis vinifera, and P. euphratica constructed by the neighbor-joining method in MEGA-X. The numbers at nodes represent bootstrap values after 1000 iterations. Each group is indicated by a different color.

Figure 3

Gene structure of aspartic proteases genes in P. euphratica. Untranslated regions (UTR) and coding sequence (CDS) are indicated by green, red and blue frames on the right, respectively. The number on the gray line represents the number of introns. Different colored frames represents different protein motifs, and each motif has its own number.

Figure 4

Collinearity analysis of aspartic protease genes between A. thaliana and P. euphratica. Colored bars denote syntenic regions between Arabidopsis and P. euphratica AP chromosomes.

Figure 5

Expression profile of aspartic protease genes in P. euphratica under different concentrations of salt stress. Color scale at the right of the dendrogram represents expression values.

Figure 6

Distribution of cis-elements in aspartic protease gene promoters of P. euphratica. (a) Number of cis-elements detected in the promoter region of each aspartic protease gene. Elements were grouped into 7 types. (b) Distribution of biotic stress related cis-elements in aspartic protease gene promoters of P. euphratica. (c) Distribution of abiotic stress related cis-elements in aspartic protease gene promoters of P. euphratica.