Multi-omics analyses reveal the mechanisms underlying the responses of Casuarina equisetifolia ssp. incana to seawater atomization and encroachment stress

Abstract

Casuarina equisetifolia trees are used as windbreaks in subtropical and tropical coastal zones, while C. equisetifolia windbreak forests can be degraded by seawater atomization (SA) and seawater encroachment (SE). To investigate the mechanisms underlying the response of C. equisetifolia to SA and SE stress, the transcriptome and metabolome of C. equisetifolia seedlings treated with control, SA, and SE treatments were analyzed. We identified 737, 3232, 3138, and 3899 differentially expressed genes (SA and SE for 2 and 24 h), and 46, 66, 62, and 65 differentially accumulated metabolites (SA and SE for 12 and 24 h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that SA and SE stress significantly altered the expression of genes related to plant hormone signal transduction, plant-pathogen interaction, and starch and sucrose metabolism pathways. The accumulation of metabolites associated with the biosynthetic pathways of phenylpropanoid and amino acids, as well as starch and sucrose metabolism, and glycolysis/gluconeogenesis were significantly altered in C. equisetifolia subjected to SA and SE stress. In conclusion, C. equisetifolia responds to SA and SE stress by regulating plant hormone signal transduction, plant-pathogen interaction, biosynthesis of phenylpropanoid and amino acids, starch and sucrose metabolism, and glycolysis/gluconeogenesis pathways. Compared with SA stress, C. equisetifolia had a stronger perception and response to SE stress, which required more genes and metabolites to be regulated. This study enhances our understandings of how C. equisetifolia responds to two types of seawater stresses at transcriptional and metabolic levels. It also offers a theoretical framework for effective coastal vegetation management in tropical and subtropical regions.

Keywords: Casuarina equisetifolia; Metabolome; Seawater atomization; Seawater encroachment; Transcriptome.

Fig. 1

DEGs in four contrasts. (a) Summary of the numbers of DEGs in four contrasts. (b) Venn diagram representation of the numbers of DEGs between two contrasts. (c) Cluster analysis of common DEGs in four contrasts. (d) KEGG pathway analysis of DEGs in the top three clusters. DEGs: Differentially expressed genes; KEGG: Kyoto Encyclopedia of Genes and Genomes

Fig. 2

Genes involved in plant hormone signal transduction in C. equisetifolia after exposure to SA and SE stress for 2 and 24 h. The original figure of plant hormone signal transduction pathway was cited from the Kanehisa laboratories [95]. Blue asterisks indicated genes with significantly down-regulated expression and red asterisks indicated genes with significantly up-regulated expression. SA: Seawater atomization; SE: Seawater encroachment; AUX1: Auxin resistant 1; AUX/IAA: Auxin/indole-3-acetic acid; ARF: Auxin response factor; GH3: Gretchen Hagen 3; SAUR: Small auxin-up RNA; CRE1: Cytokinin response 1; AHP: Arabidopsis histidine phosphotransfer proteins; A-ARR: Type-A Arabidopsis response regulator; PYL: Pyrabactin resistance 1-like; PP2C: Protein phosphatase 2 C; Sucrose non-fermenting-1-related protein kinase 2; ABF: ABA-responsive element binding factor; COI1: Coronatine insensitive 1; JAZ: Jasmonate ZIM-domain; MYC2: Myelocytomatosis proteins 2

Fig. 3

Genes involved in the plant–pathogen interaction pathway in C. equisetifolia after exposure to SA and SE stress for 2 and 24 h. The original figure of plant–pathogen interaction pathway was cited from the Kanehisa laboratories [96, 97]. Red asterisks indicated genes with significantly up-regulated expression. SA: Seawater atomization; SE: Seawater encroachment; CDPK: Calcium-dependent protein kinase; Rboh: Respiratory burst oxidase homolog; CAM/CML: Calmodulin/calmodulin-like proteins; NOS: Nitric oxide synthase; MPK4: Mitogen-activated protein kinase 4; MPK3: Mitogen-activated protein kinase 3; PR1: Pathogenesis related protein-1

Fig. 4

Genes and DAMs involved in the phenylpropanoid biosynthesis pathway in C. equisetifolia after exposure to SA and SE stress for 2 and 24 h for genes, and for 12 and 24 h for metabolites (values are relative to exposure for 0 h). The original figure of phenylpropanoid biosynthesis pathway was cited from the Kanehisa laboratories [96, 97]. Blue asterisks indicated genes with significantly down-regulated expression and red asterisks indicated genes with significantly up-regulated expression. DAMs: Differentially accumulated metabolites; SA: Seawater atomization; SE: Seawater encroachment; PAL: Phenylalanine ammonia lyase; 4CL: 4-coumarate-CoA ligases; CYP73A: Cinnamate 4-hydroxylase; HCT: Hydroxycinnamoyl transferase; CCR: Cinnamoyl-CoA reductase; COMT: Caffeic acid O-methyltransferase; CAD: Cinnamyl alcohol dehydrogenase

Fig. 5

Genes and DAMs involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, and biosynthesis of amino acids in C. equisetifolia after exposure to SA and SE stress for 2 and 24 h for genes, and 12 and 24 h for metabolites (values are relative to exposure for 0 h). The original figure of starch and sucrose metabolism, glycolysis/gluconeogenesis, and biosynthesis of amino acids pathway was cited from the Kanehisa laboratories [96, 97]. Blue asterisks indicated genes with significantly down-regulated expression and red asterisks indicated genes with significantly up-regulated expression DAMs: Differentially accumulated metabolites; SA: Seawater atomization; SE: Seawater encroachment; otsB: Trehalose-6-phosphate phosphatase; TPS: Terpene synthase; SUS: Sucrose synthase; INV: Invertase