Comparative genomic analysis of <italic>AaCOI1</italic> genes in two haplotypes HAN1 and LQ9 <italic>Artemisia annua</italic>

<x>Abstract</x> <sec> <title>Objective</title> This study aimed to elucidate the molecular mechanisms underlying the increased artemisinin content and enhanced density of glandular secretory trichomes (GSTs) in the HAN1 (Hainan) haplotype of <italic>Artemisia annua</italic>. </sec> <sec> <title>Methods</title> Employing genetic and phylogenetic analyses, we identified <italic>AaCOI1</italic> genes genome-wide, compared plant height, artemisinin content, and GST density in HAN1 and LN (Liaoning) haplotypes, elucidated their evolution and structural features, and analyzed expression of <italic>AaCOI1</italic> and associated genes. </sec> <sec> <title>Results</title> Compared to LN, HAN1 exhibited significantly greater plant height, higher artemisinin content, and increased GST density. Orthologous gene analysis identified 17,724 core genes, 21,608 dispensable genes, and 1,645 private genes. Functional identification revealed that private genes in HAN1 were enriched in functions related to insect response, whereas those in shandong were associated with cell growth and differentiation. Pronounced divergence between HAN1 and LQ9 (Shandong) was observed in <italic>AaCOI1</italic> gene sequence homology, exon–intron structure, motif composition, and <italic>cis</italic>-regulatory elements. Furthermore, HAN1 showed marked upregulation of <italic>AaCOI1</italic> genes and key artemisinin biosynthetic regulators, along with downregulation of jasmonic acid (JA) signaling repressors. </sec> <sec> <title>Conclusions</title> This study shows <italic>AaCOI1</italic> genes are multi-copy. Haplotype analysis reveals population variation in artemisinin regulation and links haplotypic divergence to differential JA response. These findings address critical knowledge gaps, offer molecular breeding targets, and promote a shift toward systems biology. The molecular mechanisms for elevated artemisinin and GST density in HAN1 were revealed. Structural variations upregulate <italic>AaCOI1</italic> genes, promoting interaction with JA signaling components like jasmonate ZIM-domain repressors (JAZs), Similar to Glycogen Synthase Kinase, Cullin-1, and Cullin-2. This suppresses JA repressors, activates the pathway, and upregulates genes for artemisinin biosynthesis and GST development, enhancing both traits. These results confirm that elevated expression of <italic>AaCOI1</italic> genes boosts artemisinin biosynthesis. </sec>