The genome of the allotetrapolyploid Morinda citrifolia (Noni) provides insights into its evolution and antioxidant function

Morinda citrifolia (Noni, 2 n = 4x=44), an allotetraploid plant from Rubiaceae family, is renowned for its antioxidant, anti-inflammatory and immune-modulating properties. Nevertheless, the mechanism responsible for its antioxidant activity is still not well known. We provide a chromosome-level assembly of the Noni genome here, with the A-subgenome size of 466.73 Mb and B-subgenome size of 442.48 Mb. Comparative genomic and transcriptomic analyses highlighted functional divergence between subgenomes, accompanied by events including structural variations, gene loss and biased expression. Specifically, analysis of homoeolog expression bias revealed that subgenome B exhibited predominant expression in pathways related to oxidative activity. Karyotype evolution within Rubiaceae is characterized by two reciprocally translocated chromosome arms (RTAs). These RTAs were common to Ophiorrhiza. pumila , M. officinalis , and M. citrifolia . We inferred that these RTAs occurred prior to the divergence of Ophiorrhiza and Morinda , followed by a polyploidization event, shaping the extant chromosome configuration of M. citrifolia . Metabolomic profiling of flavonoids across different fruit development stages, coupled with transcriptome data of relevant gene families, unveiled dynamic flavonoid compositional shifts, suggesting flavonoids are closely associated with the maturity of Noni fruit. Collectively, our findings elucidate the genetic basis of Noni's antioxidant properties and offer a valuable reference genome for advancing genetic and evolutionary research, as well as for the novel Noni varieties breeding. • A chromosome-level Noni genome assembly featuring A and B subgenomes. • Subgenome B shows specific expression in oxidative activity pathways. • Rubiaceae karyotype evolution is driven mainly by Chr3 rearrangements. • The antioxidant functions of Noni fruit are likely mediated by flavonoids.