{
  "abstract": "Background\n\nIdentifying the key genes and transcription factors involved in essential oil production in Rosa damascena is an important step toward understanding the molecular mechanisms underlying essential oil biosynthesis. Such knowledge may be applied in breeding programs aimed at improving both the yield and quality of essential oil.Results\n\nTranscriptomic profiles of two R. damascena genotypes were initially characterized using RNA-Seq followed by de novo transcriptome assembly. De novo transcriptome assembly was conducted using four assemblers. Among these assemblers, Trinity showed the best overall performance, generating the highest number of high-quality unigenes. Comparative transcriptomic analysis revealed distinct expression profiles between the two contrasting genotypes. Gene Ontology (GO) classification indicated that catalytic activity and binding were the predominant categories within the molecular function group. Similarly, metabolic and cellular processes were the most represented categories within biological processes. Key genes involved in monoterpene biosynthesis (NUDX1, HMGCS, ispH, GCPE, GPS) were significantly upregulated in genotype G2, while FDPS, TPS, and GGPS showed higher expression in genotype G1. Additionally, members of the MYB and NAC transcription factor families were markedly upregulated in genotype G2, suggesting their potential involvement in the regulation of essential oil biosynthesis.Conclusions\n\nThis study provides comprehensive insights into the transcriptomic basis of essential oil production in R. damascena. The high essential oil-producing genotype (G2) exhibited enhanced expression of genes associated with the monoterpene biosynthetic pathway, including HMGCS and GPS. MYB and NAC transcription factors were also significantly upregulated in G2. Furthermore, the reduced accumulation of sesquiterpenoids in G2 may be associated with preferential utilization of shared metabolic precursors by the monoterpenoid pathway. These findings identify promising candidate genes and transcription factors for future functional studies and metabolic engineering approaches aimed at improving essential oil yield and quality.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran.",
    "Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran. shokrpour@ut.ac.ir.",
    "Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, 1983969411, Iran.",
    "Department of Agronomy and plant breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Hamid Ahadi"
    },
    {
      "affs": [
        1
      ],
      "name": "Majid Shokrpour"
    },
    {
      "affs": [
        0
      ],
      "name": "Reza Fatahi"
    },
    {
      "affs": [
        2
      ],
      "name": "Mohammad Hossein Mirjalili"
    },
    {
      "affs": [
        3
      ],
      "name": "Mohammad Reza Naghavi"
    },
    {
      "affs": [
        0
      ],
      "name": "Morteza Sheikh-Assadi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ap5qc3n0cnxs4.bib",
  "cited_by": 1,
  "doi": "10.1186/s12870-026-09650-z",
  "fulltext_url": "https://europepmc.org/articles/PMC13718136",
  "id": "ap5qc3n0cnxs4",
  "issns": [
    "1471-2229"
  ],
  "landing_url": "https://europepmc.org/article/MED/42958049",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Research"
    ],
    [
      "openalex",
      "1312|Plant biochemistry and biosynthesis"
    ]
  ],
  "openalex": "W7172200458",
  "pdf_url": "https://europepmc.org/articles/PMC13718136?pdf=render",
  "pmcid": "PMC13718136",
  "pmid": "42958049",
  "published": "2026-08-03",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/ap5qc3n0cnxs4.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T00:20:47Z",
      "native_id": "MED:42958049",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42958049"
    },
    {
      "first_seen": "2026-11-02T12:22:15Z",
      "native_id": "PMC13718136",
      "source": "pmc",
      "url": "https://doi.org/10.1186/s12870-026-09650-z"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Plant biochemistry and biosynthesis",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Transcriptome analysis of damask rose (Rosa damascena Mill.) petals: unveiling the genetic basis of essential oil biosynthesis.",
  "title_text": "Transcriptome analysis of damask rose (Rosa damascena Mill.) petals: unveiling the genetic basis of essential oil biosynthesis.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:15Z",
  "url": "https://research.draconitic.com/paper/ap5qc3n0cnxs4",
  "venue": "BMC plant biology",
  "versions": []
}