Conserved stress-responsive genes involved in the early development of Euterpe Edulis

Abstract

The palm tree Euterpe edulis (juçara) plays a crucial ecological and socioeconomic role in the Atlantic Forest. Its wide distribution suggests the presence of adaptive mechanisms for tolerance to abiotic factors, particularly during early developmental stages, such as water availability and shading. This study aimed to identify conserved and differentially expressed genes (DEGs) involved in the early development of E. edulis, analyzing different tissues and two divergent plant matrices. Using eight RNA-Seq libraries, the strategy was to obtain the first transcriptome for the species through reference mapping against the Elaeis guineensis genome, with focus on conserved genes, followed by differential expression and functional annotation analyses. Among the 32,000 conserved genes identified, 1,133 were differentially expressed, with 11 showing differential expression in both tissues, 678 exclusively in leaves, and 444 in roots. Genes responsive to critical stress factors during early development were identified, revealing matrix-specific environmental adaptations, as well as genes associated with metabolism, light stimuli, and structural development. Leaf tissues exhibited the highest number of exclusive DEGs, indicating greater gene modulation in this tissue. The identification of conserved and highly expressed genes constitutes the first genomic insights for E. edulis, providing a foundation for studies aimed at its management, conservation, and genetic improvement for this non-model and endangered organism.

Keywords: Arecaceae; Differential expression; Juçara; RNA-seq; Transcriptome.

Fig. 1

Euterpe edulis matrices UFES_250 (Figures A, B, and C) and Santa Marta (SM) (Figures D, E, and F). Roots and leaves from both matrices were collected after germination for RNA extraction. (A) Euterpe edulis UFES_250 during germination (three months); (B) Euterpe edulis UFES_250 after six months of germination; (C) Root (mean 13 cm) and aerial part (mean 14 cm) of E. edulis UFES_250. (D) Euterpe edulis SM during germination (three months), (E) Euterpe edulis SM after six months of germination, (F) root (mean 17 cm) and aerial part (mean 16 cm) of E. edulis SM.

Fig. 2

Flowchart of the applied methodology. Reads obtained from the FASTQ file, resulting from Illumina sequencing, were analyzed for quality and mapped to reference, resulting in 32,092 genes. After filtering, 7,140 expressed genes were obtained, which were normalized. Differential gene expression analysis was then performed, highlighting 678 differentially expressed genes (DEGs) in leaves and 444 in roots. When both tissues were analyzed, 11 DEGs were identified. All expressed genes were functionally annotated.

Fig. 3

Comparative boxplot of early development data for traits such as lengths of aerial part, leaflet, stem, and root, as well as fresh and dry weight of aerial part and root from 50 seedlings of each UFES_250 and SM matrix, after six months in a greenhouse. Significant differences are indicated by asterisks (‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05).

Fig. 4

(A) Principal component analysis (PCA) showing the general differences between expression profiles of the libraries from the different matrices UFES_250 (purple ellipse) and Santa Marta (SM) (green ellipse). (B) The relative abundance of the 7,000 normalized genes in leaves and roots of the UFES_250 and SM matrices in individual and hierarchical clustering, describing the clustering between expression profiles in the analyzed tissues. Legend: RP1- Root pool 1; RP2- Root pool 2; LP1- Leaf pool 1; LP3- Leaf pool 3.

Fig. 5

Venn diagram representing exclusive and shared genes by matrix and tissue. (A) Result of the 7,140 genes identified in the analysis of all eight libraries combined, showing the number of genes exclusive to leaf tissue (92) and root tissue (670) and by matrix (UFES_250 and Santa Marta - SM). (B) Result of the 4,239 genes identified in the analysis of only the leaf libraries, showing the number of exclusive genes in the UFES_250 (368) and SM (174) matrices. C- Result of the 6,052 genes identified in the analysis of only the root libraries, showing the number of exclusive genes in the UFES_250 (274) and SM (130) matrices.

Fig. 6

Differentially expressed genes (DEGs) between UFES_250 and Santa Marta (SM) matrices. On the left, volcano plots of the DEGs. The y-axis represents the significant gene expression level between samples, measured by the p-value, while the x-axis represents the DEGs’ fold change (logFC). Blue and red points indicate down-regulated and up-regulated genes, respectively. Gray points represent genes with no significant differential expression. On the right, heatmaps of down-regulated and up-regulated genes with higher log2 FC values. The color indicates the expression level of DEGs with log2. (A) Result of the 11 DEGs obtained from the analysis of all tissues together, six up-regulated and five down-regulated in UFES_250. (B) Result of the 678 DEGs obtained from the analysis of only leaf tissue, 285 up-regulated and 393 down-regulated in UFES_250. (C) Result of the 444 DEGs obtained from the analysis of only root tissue, 119 up-regulated and 325 down-regulated in UFES_250. Legend: RP1- Root pool 1; RP2- Root pool 2; LP1- Leaf pool 1; LP3- Leaf pool 3.

Fig. 7

Analysis of the main Gene Ontology (GO) of differentially expressed genes (DEGs) from the UFES_250 and Santa Marta (SM) matrices of Euterpe edulis, categorized into ‘biological process’ (green), ‘cellular component’ (blue), and ‘molecular function’ (orange). A. All tissues combined. B. Leaf tissue. C. Root tissue. D. Venn diagram of DEGs showing the distribution of tissue-specific and tissue-independent GOs in the two tissue sets (leaf and root).

Fig. 8

Gene Ontology (GO) analysis of genes that are not differentially expressed from the UFES_250 and Santa Marta (SM) matrices of Euterpe edulis, categorized into ‘biological process’ (green), ‘cellular component’ (blue), and ‘molecular function’ (orange), considering A. both tissues; B. leaf tissue; C. root tissue.