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. 2021 Dec 27;13(1):67.
doi: 10.3390/genes13010067.

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells

Deheng Yao  1 , Zihao Zhang  1 , Yukun Chen  1 , Yuling Lin  1 , Xuhan Xu  1 , Zhongxiong Lai  1
Affiliations

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells

Deheng Yao et al. Genes (Basel). .

Abstract

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes' change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary.

Keywords: MeJA; RNA-seq; Rosmarinus officinalis Lour.; antioxidant enzymes; qRT-PCR; suspension cells; transcription factors.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Physiological and biochemical indicators of rosemary suspension cells under different concentrations of MeJA. (A) changes in PAL activities. (B) changes in SOD activities. (C) changes in POD activities. (D) changes in CAT activities. (E) changes in PPO activities. (F) changes in MDA contents. (G) changes in H2O2 contents. (H) changes in proline contents. Values represent means ± SDs of three replicates. Different lower-case letters indicate statistically significant differences at the 0.05 level by one-way ANOVA with Duncan’s test.
Figure 2
Figure 2
Statistical analysis of differentially expressed unigenes in rosemary suspension cells under different concentrations of MeJA. (A) The Venn diagram of expressed genes in four MeJA treatments. (B) statistic of up/down-regulated genes in pairwise comparisons. (C) Venn diagram of DEGs under MeJA treatment. (D) Venn diagram of the unique and common regulated DEGs up-regulated of DEGs under MeJA treatments. (E) Venn diagram of the unique and common regulated DEGs down-regulated of DEGs under MeJA treatments.
Figure 3
Figure 3
GO-terms enrichment analysis. From the red to blue corresponds to the numerical value of corrected Q and significant enriched GO-terms from the low to the high. (A) biological process; (B) cellular component; (C) molecular function.
Figure 4
Figure 4
The top 20 KEGG pathways enriched by DEGs in in the comparisons. Red indicates significant enrichment and gray indicates no significant enrichment.
Figure 5
Figure 5
DEGs assigned to phenylpropanoid and flavonoid biosynthesis pathways under MeJA treatments. (A) heat map of the expression of DEGs in phenylpropanoid biosynthesis. (B) simplified diagram of phenylpropanoid and flavonoid biosynthetic pathway. (C) heat map of the expression of DEGs in flavonoid biosynthesis.
Figure 6
Figure 6
DEGs assigned to terpenoid biosynthesis pathway under MeJA treatments. (A) simplified diagram of the terpenoid biosynthesis pathway. (B) heat map of the expression of DEGs related to terpenoid backbone biosynthesis pathway.
Figure 7
Figure 7
TFs in rosemary suspension cells under MeJA treatments. (A) classification statistics of TFs. (B) the Frequency distribution of differentially expressed TFs. (C) cluster analysis of expression profiles of TFs. (D) statistic of differentially TFs in the comparisons of CKvsM10. (E) statistic of differentially expressed TFs in the comparisons of CKvsM50. (F) statistic of differentially expressed TFs in the comparisons of CKvsM100.
Figure 8
Figure 8
qRT-PCR verification of DEGs in rosemary suspension cells responding to MeJA.
Figure 9
Figure 9
Schematic representation of rosemary suspension cells responding to MeJA. Antioxidant enzymes and non-enzymes, DEGs of many biosynthesis pathways played an essential beneficial in rosemary suspension cells responding to MeJA. Red indicates the key biosynthesis and signals transduction pathways, italics indicate key DEGs.
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