Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis

Phellodendron amurense is a Tertiary relict species with significant ecological and medicinal value. Here, we present a near telomere-to-telomere (T2T) genome assembly for this species. The assembled genome is 2.92 Gb, with a contig N50 length of 65.3 Mb, and contains 59,548 protein coding genes. Evolutionary analysis reveals that P. amurense is a paleooctoploid and the four subgenomes derived from the hybridizations of four parental lineages. We dissect the berberine biosynthesis pathway in the genome and identify the CNMT gene family (PaCNMT), which may contribute to the berberine biosynthesis in P. amurense. The PaCNMT family underwent a gene loss event within the Rutaceae lineage, followed by functional re-emergence in the P. amurense lineage through LTR-mediated gene expansion, which could have shaped the metabolic pathway in P. amurense. Our results provide insights into berberine biosynthesis in woody plants and highlight the role of LTR retrotransposons in driving the evolution of specialized metabolism.