Analysis of a near telomere-to-telomere genome of Cinnamomum cassia (L.) J. Presl uncovers the genetic mechanism of a phenylpropanoid pathway during phloem development
Year: 2026
Type: article
Abstract: Cinnamomum cassia (L.) J. Presl is a medicinal and edible plant in the Lauraceae family that is extensively utilized in medicine, health supplements, food, spices, cosmetics, and postharvest fruit and vegetable preservation. However, the molecular mechanisms governing the accumulation of its key differential metabolites and the developmental regulation of its phloem tissue used for medicinal purposes remain largely unexplored due to the absence of a reference genome. To address this gap, the first near telomere-to-telomere (T2T), chromosome-scale genome of C. cassia was assembled by integrating PacBio HiFi, Oxford Nanopore, Illumina, and high-throughput chromatin conformation capture (Hi-C) sequencing technologies, revealing a diploid genome of 1158.36 Mb. Transcriptomic and metabolomic analyses were performed on multiple tissues of C. cassia and its botanical variety Cinnamomum cassia Presl var. macrophyllum Chu to characterize tissue-specific accumulation patterns of differential metabolites. To elucidate the regulatory networks coordinating differential metabolite accumulation with phloem development across seasonal growth cycles, a time-ordered gene co-expression network (TO-GCN) analysis and weighted gene co-expression network analysis (WGCNA) were applied to time-series transcriptomic, metabolomic, and hormone profiling data. Through this integrative approach, candidate dual-function transcription factors that potentially co-regulate phenylpropanoid biosynthesis and phloem thickening were identified. These findings provide the first genomic resource for C. cassia and establish a mechanistic framework for understanding the coordinated regulation of differential metabolite accumulation and phloem development, offering valuable targets for future molecular breeding aimed at improving both medicinal quality and yield.
Source: Industrial Crops and Products
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,720
OpenAlex ID: W7223461678