Genome-Wide Identification and Expression Analysis of PP2C Gene Family in Eelgrass

Abstract

Background: Protein Phosphatase 2C (PP2C), a conserved family in plants, plays a crucial role in ABA and MAPK signaling pathways. Its functional diversity provides key mechanisms for plants' adaptation to environmental changes. However, research on PP2C family members remains significantly underexplored in seagrasses, which are model organisms adapted to complex marine environments.

Methods: In this study, we systematically analyzed the PP2C gene family in eelgrass using bioinformatic methods and performed a qPCR experiment to verify the expression of a few members in their response to salt stress.

Results: The eelgrass PP2C gene family comprises 52 members, categorized into 13 subfamilies. Most PP2C genes exhibit a differential expression across various organs, with some members showing significant organ specificity. For instance, 12 members are specifically highly expressed in male flowers, suggesting that PP2Cs may function in male flower development. Additionally, four members (ZosmaPP2C-04, ZosmaPP2C-07, ZosmaPP2C-15, and ZosmaPP2C-18) in eelgrass are up-regulated under salt stress, with a qPCR confirming their response. The syntenic genes of ZosmaPP2C-15 and ZosmaPP2C-18 were identified across multiple species, indicating their evolutionary conservation. Numerous response elements associated with plant hormones and stress were identified within the promoter sequences of eelgrass PP2C genes. Notably, the promoter regions of salt-responsive genes are rich in the ABRE, implying that ABA may participate in regulating the expression of these PP2Cs. Furthermore, the predictive analysis of protein interactions suggests the potential existence of the ABA core signaling module PYL-PP2C-SnRK2 in eelgrass.

Conclusions: This study provides a new insight for understanding the biological functions of the PP2C family in eelgrass, which is important for elucidating the mechanisms of its growth, development, and environmental adaptability.

Keywords: ABA; PP2C; eelgrass; male flower; salt stress.

Figure 1

Chromosomal localization of eelgrass PP2Cs.

Figure 2

Phylogenetic tree of PP2Cs in eelgrass and A. thaliana. The colors represent different groups of PP2Cs. Blue circles represent A. thaliana genes, and red circles represent eelgrass genes.

Figure 3

Conserved protein motifs of eelgrass PP2Cs.

Figure 4

Synteny analysis of eelgrass PP2Cs.

Figure 5

The expression analysis of eelgrass PP2Cs. (a) Expression profiles of organ-specific PP2Cs in eelgrass; (b) expression profiles of salt-responsive PP2Cs in eelgrass; and (c) the validation of 4 eelgrass PP2Cs in response to the salt stress by the qPCR. Three tissues (leaf, stem, root) were analyzed under two salinity conditions: 30 (control) and 50 (high salinity). The star marks on statistical charts represent the statistical significance: “*” stands for p-value < 0.05, “**” stands for p-value < 0.01, “***” stands for p-value < 0.001.

Figure 6

The cis-acting regulatory element of eelgrass PP2Cs on the promoter region. (a) Bar plots showing the number of PP2Cs that contain a specific motif and box plots showing the number of specific motifs on the promoter of PP2C genes. (b) The count of specific motifs on the promoter region of each PP2C gene.

Figure 7

Potential PYL-PP2C-SnRK2 modules in eelgrass. (a) The prediction of PP2C-interacting proteins in eelgrass. The blue dots represent genes of A. thaliana, the green dots represent genes of rice, the orange dots represent genes of maize, and the pink represent genes of eelgrass. Solid lines represent the interactions documented in the STRING database, whereas dashed lines illustrate the mapping relationships between the eelgrass genes and those recorded in the database. (b) Organ-specific expression patterns of PYL and SnRK2 family members in eelgrass.