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Using the camphor reference genome, stem transcriptomes and metabolomes were profiled across four developmental stages in linalool- and borneol-type trees to identify genes driving secondary cell wall deposition and terpenoid pathways. WGCNA highlighted phenylpropanoid and starch/sucrose metabolism enrichment, while lignin biosynthesis gene expression suggested chemotype-specific lignification timing, including distinct bypass and terpenoid precursor routing.",{"@graph":14,"@context":72},[15,34,55],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & 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research question does the study address?","Question",{"text":62,"@type":63},"The study investigates how transcriptomics and metabolomics can reveal genes and pathways underlying secondary cell wall deposition and terpenoid biosynthesis during Camphora officinarum stem development.","Answer",{"name":65,"@type":60,"acceptedAnswer":66},"How were developmental stages and chemotypes handled in the analysis?",{"text":67,"@type":63},"Stem transcriptomes and metabolomes were profiled across four developmental stages in linalool-type and borneol-type camphor trees to compare chemotype-specific processes.",{"name":69,"@type":60,"acceptedAnswer":70},"What does WGCNA contribute to the findings?",{"text":71,"@type":63},"Weighted Gene Co-expression Network Analysis identified enriched pathways, especially phenylpropanoid and starch/sucrose metabolism, supporting active secondary cell wall formation during 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BMC Genomics (2026) 27:6 BMC Genomics  \n[https://doi.org/10.1186/s12864-025-12266-6](https://doi.org/10.1186/s12864-025-12266-6)  \nRESEARCH Open Access  \nIntegration of transcriptomics   \nand metabolomics provides insights into secondary cell wall deposition and terpenoid biosynthesis during stem development in Camphora officinarum  \nJiexi Hou 1, Qian Zhang2, Rongtao Wang 1, Jun Yao2, Yonglin Zhong2, Yuanfang Zhong3, Junfa Wei4, Lizhong Liu5, Zhinong Jin 1 and Chen Hou2*  \nAbstract  \nCamphora officinarum Nees (Cinnamomum camphora) has traditionally been cultivated as bushes for essential oil extraction from its leaves and twigs (small stems) . terpenoid deposition in leaves is well-studied, While the stems have received less attention. Using the camphor tree reference genome, we profiled stem transcriptomes and metabolomes across four developmental stages in linalool-and borneol-type camphor trees to elucidate key genes underlying secondary cell wall deposition and terpenoid biosynthesis. Weighted Gene Co-expression Network Analysis (WGCNA) highlighted enrichment of phenyl propanoid and starch and sucrose metabolism pathways, consistent with active secondary cell wall formation. Expression of the full complement of lignin biosynthesis genes, including those participating in non-conserved bypass routes (e. g., CSE, C4H, and C3'H), indicated chemotype-specific timing of lignification (earlier in the linalool-type) . Across development, downshifts in GPPS, FPPS, and GGPPS expressions were observed in both chemotypes, whereas their precursor supply appeared to favor distinct routes: DXS (MEP pathway) was identified in the linalool-associated co-expression modules, while HMGCR (MVA pathway) was identified in the borneol-associated modules; elevated ACAT further typified the borneol type. Regulatory programs also diverged: WGCNA associated brassinosteroid-linked genes with the linalool-type and cytokinin-linked genes with the borneol-type; comparative analysis revealed that ERF026 and SHR2 were upregulated in the linalool-type, whereas bHLH068, bHLH093, and WRKY40 were upregulated in the borneol-type. Overall, these findings provide insights into lignocellulosic biomass formation and terpenoid biosynthesis during stem development, highlighting key drivers of chemotype diversity in C. officinarum.  \nKeywords Camphora officinarum, Secondary cell wall deposition, Terpenoid biosynthesis, WGCNA, Chemotype diversity  \n*Correspondence: Chen Hou [houchen@sinogaf.cn](houchen@sinogaf.cn)  \nFull list of author information is available at the end of the article  \n© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit [http://creati](http://creati)[vecommons.org/l](vecommons.org/l)icenses/by-nc-nd/4.0/.  \nHou et al. BMC Genomics (2026) 27:6  \nIntroduction  \nCamphor trees (Camphora officinarum Nees; syn. Cinnamomum camphora), known for their rich terpenoid and essential oil content, hold significant economic value due to their wide-ranging applications in the pharmaceutical, fragrance, and insect repellent industri","cbCaime20D5WsaEK","https://ap.wps.com/l/cbCaime20D5WsaEK","pdf",8757683,"English","# Abstract\n# Introduction","[{\"question\":\"What research question does the study address?\",\"answer\":\"The study investigates how transcriptomics and metabolomics can reveal genes and pathways underlying secondary cell wall deposition and terpenoid biosynthesis during Camphora officinarum stem development.\"},{\"question\":\"How were developmental stages and chemotypes handled in the analysis?\",\"answer\":\"Stem transcriptomes and metabolomes were profiled across four developmental stages in linalool-type and borneol-type camphor trees to compare chemotype-specific processes.\"},{\"question\":\"What does WGCNA contribute to the findings?\",\"answer\":\"Weighted Gene Co-expression Network Analysis identified enriched pathways, especially phenylpropanoid and starch/sucrose metabolism, supporting active secondary cell wall formation during development.\"}]","Integration of transcriptomics and metabolomics provides insights into secondary cell wall deposition and terpenoid biosynthesis during stem development in Camphora officinarum | PDF",1790700960]