Clausena lansium genome provides new insights into alkaloid diversity and evolution of the methyltransferase family

Wampee (Clausena lansium) native to southern China, is an important evergreen fruit tree that has a long history of use for medicinal purposes. Here, a chromosome-level genome of C. lansium was constructed with a genome size of 282.9 Mb and scaffold N50 of 30.75 Mb. The assembled genome contains 48.70% repetitive elements and 24,381 protein-coding genes. Comparative genomic analysis showed that C. lansium diverged from Aurantioideae 15.91-24.95 million years ago. Additionally, some expansive and specific gene families related to methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity were also identified. Further analysis indicated that N-methyltransferase (NMT) was mainly involved in alkaloid biosynthesis and O-methyltransferase (OMT) participates in the regulation of coumarin accumulation in wampee. This suggested that wampee rich in alkaloids and coumarins might be due to the gene expansions of NMT and OMT. The tandem repeat event was one of the major reasons for NMT expansion. Hence, the reference genome of C. lansium will benefit the identification of some useful medicinal compounds from wampee resources and reveal their biosynthetic pathways.