Fig 1.
The rhizomes and volatile oils of Curcuma wenyujin from Wenzhou and Haikou.
Fig 2.
Paraffin sections of Curcuma wenyujin rhizomes showing starch (potassium iodide staining) (a, b) and oil cells (PAS reaction) (c, d) in rhizomes from Wenzhou (b, d) and Haikou (a, c) observed under a biological microscope (a, b scale = 50 μm; c, d scale = 100 μm).
Fig 3.
The content of oil, curcumin, polysaccharide, and starch in Curcuma wenyujin rhizomes produced in Wenzhou and Haikou.
Fig 4.
A Gene Ontology (GO) histogram of the classification of annotated unigenes that were differentially expressed between Wenzhou (WZ) and Haikou (HK) rhizomes.
The red, green, and blue histograms represent the differentially expressed genes (DEGs) in the different sub-categories, whereas the light red, green, and blue histograms represent the annotated unigenes. The right-hand Y-axis represents the number of annotated genes or DEGs in the main categories, and the left-hand Y-axis represents the percentage of annotated unigenes or DEGs in the main categories.
Fig 5.
Annotation of unique sequences (1,597) based on KEGG classification.
Fig 6.
Differential expression of the unique genes in Curcuma wenyujin rhizomes obtained from Wenzhou (WZ) and Haikou (HK).
Green and red dots denote genes with significantly different expression (FDR < 0.01), with green indicating down-regulated genes, red indicating up-regulated genes, and black indicating those genes showing no significantly different expression.
Fig 7.
Cluster analysis of genes that were differentially expressed (4,620) between Wenzhou (WZ) and HK (HK) rhizomes.
Red and green represent up- and down-regulated genes, respectively, in Wenzhou (WZ) rhizomes compared with those of Haikou (HK). The heatmap was produced based on fragments per kilobase per million (FPKM) data.
Fig 8.
Clusters of Orthologous Group (COG) functional classification of the consensus sequences of genes that are differentially expressed between Wenzhou (WZ) and Haikou (HK) rhizomes.
Fig 9.
Enrichment of KEGG pathways with genes that were differentially expressed between Wenzhou (WZ) and Haikou (HK) rhizomes.
Pathway name and enrichment intensity are shown in the right-hand legend. The Q value is the corrected P-value (false discovery rate). The enrichment factor is the ratio of the number of differentially expressed genes (DEGs) in a pathway to the number of all genes in that pathway. (a, all DEGs; b, up-regulated DEGs; c, down-regulated DEGs).
Fig 10.
qRT-PCR verification of genes that were differentially expressed between Wenzhou (WZ) and Haikou (HK) rhizomes (a) and the corresponding verification based on RNA-seq (b).
Using c121677 as a control/reference gene, the relative expression of genes was calculated using the 2-ΔΔCt method. Asterisks denote significant differences (*, P < 0.05; **, P < 0.01; ***, P < 0.001). Error bars represent the standard deviations of mean values (n = 6). (CHS2: chalcone synthase2; CHS1: chalcone synthase1; TT4: chalcone and stilbene synthase family protein; LPS: levopimaradiene synthase; CDS/LIS: 3S-linalool synthase; ISPS: isoprene synthase; TPS06: dolabella-3,7-dien-18-ol synthase/sesquiterpene synthase 6; GAE: UDP-glucuronate 4-epimerase; PME: pectin methylesterase; BGLU: beta-glucosidase; SUS: sucrose synthase; TSTA: GDP-l-fucose synthase; GALE: UDP-glucose 4-epimerase; GH: glycoside hydrolase; LOC103985749: uncharacterized protein LOC103985749).