What question did this study set out to answer?

The research aims to explore the genomic basis and organ-specific metabolic functions of Clinacanthus nutans.

February 25, 2026Open Access

From folklore to explore: integrating genomic and multi-omics data for Clinacanthus nutans provides insights into the evolution and organ-specific therapeutic basis

Key Points

The research aims to explore the genomic basis and organ-specific metabolic functions of Clinacanthus nutans.
Assembled the first chromosome-scale genome of Clinacanthus nutans.
Conducted phylogenomic analysis to identify whole-genome duplication events.
Performed integrated transcriptomic and metabolomic analyses across five different organs.
Applied weighted gene co-expression network analysis (WGCNA) to identify key regulatory genes.
Identified a large genome primarily composed of repetitive elements.
Revealed gene family expansions in pathways relevant to flavonoid and triterpenoid biosynthesis.
Demonstrated pronounced gene expression differences between leaves and roots.
Highlighted key genes and transcription factors involved in organ-specific metabolic regulation.

Abstract

Abstract Clinacanthus nutans is a traditional medicinal plant widely used in Southeast Asia for treating inflammation, viral infections, and cancer. However, its molecular basis remains poorly understood. In this study, the first chromosome-scale genome of C. nutans (731.61 Mbp) was assembled, with 93.76% anchored to 18 pseudochromosomes. Repetitive elements constituted 69.05% of the genome, predominantly long terminal repeat (LTR) retrotransposons. Phylogenomic and synonymous substitution rate (Ks) analyses revealed a Lamiales-wide whole-genome duplication (WGD) event, followed by extensive chromosomal rearrangements. Gene family expansion analysis showed that segmental and dispersed duplications were the primary drivers of enzyme-coding genes (EGs) expansion involved in the flavonoid and triterpenoid pathways. Integrated transcriptomic and metabolomic analyses across five organs revealed distinct organ-specific expression and metabolite profiles. Genes exhibited pronounced differential expression between leaves and roots, with enrichment in flavonoid and triterpenoid biosynthetic pathways, highlighting functional divergence and metabolic specialization. Flavonoids were enriched in aerial tissues, whereas triterpenoids accumulated in roots. Weighted gene co-expression network analysis (WGCNA) identified key EGs (e.g., CHS, CHI, OSC) and core transcription factors (TFs) (e.g., MYB, bHLH, WRKY) potentially involved in organ-specific metabolic regulation. These findings suggest a coordinated transcriptional-metabolic regulatory framework underlying the specialized functions of different tissues. This work provides valuable genomic resources and mechanistic insights into the biosynthesis and regulation of bioactive compounds in C. nutans, thereby facilitating future research and molecular breeding of this important ethnomedicinal plant.

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