Large-scale plant genomic identification and analysis uncover <i>ASMT/COMT</i> copy number variation driving melatonin dosage balance

ASMT/COMT, as a key rate-limiting enzyme regulating melatonin biosynthesis, has garnered significant attention. This study investigates the evolutionary mechanisms of the <i>ASMT/COMT</i> gene family in melatonin biosynthesis. A total of 28 010 <i>ASMT/COMT</i> genes from 1052 species were identified through an integrated approach combining large-scale identifications and analyses. At the pan-genome level, we identified 5186, 336, 2137, and 1814 <i>ASMT/COMT</i> genes respectively in <i>Triticum aestivum</i>, <i>Aegilops tauschii</i>, diploid and tetraploid <i>Solanum tuberosum</i> haplotype genomes (247, 86, 670, and 96 orthologous gene groups). Expansion patterns of the <i>ASMT/COMT</i> gene family were explored through synteny networks in 104 Poaceae and 88 Solanaceae plants. Further investigation of copy number variation (CNV) in the 1052 species, along with a focused analysis of hexaploid wheat and its diploid progenitor <i>Ae. tauschii</i>, indicated a functional divergence linked to gene dosage. The catalytically efficient COMT is maintained at low-copy conditions, whereas the less active ASMT is amplified under high-copy conditions. Intriguingly, in polyploid potatoes, the total <i>ASMT/COMT</i> copy number was lower in tetraploids than in diploids, suggesting a distinct dosage balance mechanism operating in polyploids. In contrast, the melatonin receptor <i>CAND2</i> consistently remained in a low-copy state, with no significant correlation to <i>ASMT/COMT</i> copy number. Expression analysis revealed that <i>COMT</i> is generally expressed at higher levels than <i>ASMT</i>, highlighting a compensatory relationship between gene dosage and transcriptional regulation. Collectively, our findings uncover a dosage balance mechanism that fine-tunes melatonin biosynthetic homeostasis through coordinated CNV and expression regulation, offering a new perspective on the evolution of metabolic enzymes.