Cinnamon Tree Genome Reveals 12 JAZ Genes Tied to Essential Oil

Researchers have mapped the full family of JAZ genes in the cinnamon tree Cinnamomum burmannii, identifying 12 members that appear to sit at the crossroads of the plant’s stress responses and its production of valuable essential oils. The study, a genome-wide survey combined with gene expression profiling, is the first systematic characterization of this gene family in the species, an evergreen Lauraceae tree native to southeastern China, Indonesia, and the Philippines whose bark, leaves, and roots are rich in terpenoid volatile compounds.

JAZ proteins are central negative regulators of jasmonate signaling, a hormone pathway that governs plant growth, development, and defense against both biotic and abiotic stress. Under resting conditions, JAZ repressors bind transcription factors such as MYC2 and block the expression of jasmonate-responsive genes. When stress strikes, bioactive JA-Ile accumulates and promotes association of the SCF COI1 E3 ubiquitin ligase complex with JAZ proteins, marking them for degradation by the 26S proteasome. That releases downstream transcription factors from repression, allowing JA-responsive genes involved in stress defense and secondary metabolism to switch on. Because essential oil biosynthesis in aromatic plants is often tied to this pathway, the JAZ family is a prime suspect in regulating oil yield.

To find the genes, the team combined two search strategies against the C. burmannii genome assembly: bidirectional BLAST comparisons using Arabidopsis JAZ protein sequences as queries, and Hidden Markov Model searches for the conserved TIFY (PF06200) and CCT_2/Jas (PF09425) domains. After removing sequences with deleted or incomplete conserved domains, 12 members emerged, designated CbJAZ1 through CbJAZ12 based on their chromosomal positions. All 12 contained both the TIFY and Jas domains. The encoded proteins range from 117 to 392 amino acids, with molecular weights between 13.08 and 41.67 kilodaltons and isoelectric points from 8.78 to 9.91, meaning every member is a basic protein. All showed negative GRAVY values, indicating hydrophilic character, and instability indices above 40, predicting instability in vitro. Subcellular prediction placed every protein in the nucleus.

Phylogenetic analysis using neighbor-joining and maximum-likelihood methods, built from JAZ protein sequences of C. burmannii, poplar (Populus trichocarpa), Arabidopsis, and rice, sorted the 12 CbJAZ proteins into four subgroups following the Arabidopsis grouping system. Group IV was the largest with five members; Group II contained only CbJAZ10; Groups I and III each held three. Most CbJAZ proteins clustered more closely with poplar sequences than with those of rice or Arabidopsis, a pattern the authors attribute to the shared evolutionary history of dicotyledonous trees. Conserved motif analysis identified 10 motifs, with Motif 1 corresponding to the Jas domain and Motif 2 to the TIFY domain, both present in all 12 proteins. Exon numbers ranged from 3 to 8, and exon-intron structures largely mirrored the phylogenetic subgroups. Notably, a conserved Phase 2 intron within the Jas motif coding region, positioned at the codon for a conserved arginine, was found in eight of the 12 genes; in Arabidopsis, alternative splicing at such introns produces truncated JAZ proteins that act as dominant repressors of JA signaling because they cannot interact with COI1 but still bind MYC2.

The family’s expansion appears to have been driven almost entirely by segmental duplication. Comparative collinearity analysis identified seven segmental duplication pairs among the 12 genes and no tandem duplications at all. Cross-species synteny revealed homologous JAZ gene pairs between C. burmannii and poplar (14), Arabidopsis (12), and rice (9), with 8, 8, and 4 syntenic linkages established respectively. Two genes, CbJAZ2 and CbJAZ11, possessed orthologous syntenic blocks in all three comparison species, suggesting they are deeply conserved across angiosperms and may form core components of the jasmonate signaling machinery.

Promoter analysis of 2-kilobase upstream sequences uncovered a diverse array of cis-acting elements falling into four functional categories: light-responsive, hormone-responsive, stress-responsive, and growth- and development-related. Light-responsive motifs were the most abundant, with the G-box appearing most frequently and present in every CbJAZ gene. Hormone-responsive elements ranked second, including MeJA-responsive CGTCA/TGACG motifs, ABA-responsive ABRE elements, gibberellin-, auxin-, and salicylic acid-related motifs. ABRE elements were present in all 12 promoters. Stress-related elements included ARE, the drought-associated MBS, LTR, and TC-rich repeats.

Expression profiling by quantitative RT-PCR, using three-year-old clonal plants grown at Foshan Botanical Garden in China, revealed pronounced tissue specificity across roots, young stems, flowers, fruits, and leaves at four developmental stages. Six genes, CbJAZ1, CbJAZ6, CbJAZ7, CbJAZ8, CbJAZ9, and CbJAZ11, preferentially expressed in reproductive organs, all peaking in flowers with moderately high expression in fruits. CbJAZ2 and CbJAZ10 showed constitutive expression across all tissues, maintaining stably high levels throughout leaf development. The remaining four genes showed low basal expression with transient peaks at specific leaf stages. CbJAZ5 was highly expressed in young leaves, while CbJAZ7, CbJAZ8, and CbJAZ9 peaked at the mature leaf stage, a timing that matches the general trend of terpenoid biosynthesis increasing as leaves mature.

The team then treated seedlings with 100 micromolar methyl jasmonate, 100 micromolar abscisic acid, or 20 percent PEG 6000 to simulate drought, sampling leaves at 0, 6, 12, and 24 hours. Under MeJA, nine CbJAZ genes were upregulated to varying degrees, with CbJAZ8 and CbJAZ9 showing the most dramatic induction, more than 15-fold at 6 hours before declining. Under ABA, the pattern was largely reversed: several genes, including CbJAZ1, CbJAZ7, CbJAZ8, CbJAZ9, and CbJAZ10, were significantly repressed early and gradually recovered. Under drought, only CbJAZ1 was significantly induced at 6 hours, while eight other genes were suppressed to varying degrees. CbJAZ8 and CbJAZ9 responded significantly to all three treatments. Transient expression of CbJAZ8-GFP and CbJAZ9-GFP fusion proteins in tobacco epidermal cells confirmed nuclear localization, matching the computational prediction.

To connect signaling with metabolism, the researchers measured essential oil content in the same leaf samples by hydrodistillation. Oil content rose from 0 to 6 hours after MeJA treatment, peaked at 6 hours, and then gradually declined through 12 and 24 hours. Pearson correlation analysis identified three genes significantly correlated with oil content: CbJAZ7 (r = 0.98, p = 0.02), CbJAZ8 (r = 0.96, p = 0.04), and CbJAZ9 (r = 0.97, p = 0.03), with CbJAZ9 showing the highest coefficient. The authors suggest these genes may be closely associated with MeJA-induced essential oil accumulation in leaves, though they emphasize that the conclusions rest on expression profiling and correlation analysis alone. Direct functional evidence for the roles of CbJAZ8 and CbJAZ9 in jasmonate-ABA-drought crosstalk, and in essential oil regulation, remains to be established through protein interaction assays and genetic functional studies. The compact 12-member family, shaped by segmental duplication and retaining canonical domains, now provides a candidate gene framework for future efforts to understand and potentially improve essential oil yield in this aromatic tree.

Subject of Research: Genome-wide identification of the JAZ gene family and its stress-responsive expression in Cinnamomum burmannii

Article Title: Genome‐Wide Identification and Stress‐Responsive Expression of the JAZ Gene Family in Cinnamomum burmannii

Article References: Lin, W., Chen, X., Li, Y., Liu, X., & Cui, Z. (2026). Genome‐Wide Identification and Stress‐Responsive Expression of the JAZ Gene Family in Cinnamomum burmannii. Plant Direct, 10(10), Article e70195. https://doi.org/10.1002/pld3.70195

Image Credits: AI Generated

DOI: 10.1002/pld3.70195

Keywords: Cinnamomum burmannii, JAZ gene family, jasmonate signaling, essential oil, terpenoid biosynthesis, segmental duplication, MeJA, ABA, drought stress, phylogenetic analysis, cis-regulatory elements, qRT-PCR