A chromosome‐scale genome of Rhus chinensis Mill. provides new insights into plant–insect interaction and gallotannins biosynthesis

SUMMARY Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal‐level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase‐like (SCPL) and their homologs involved in HT production were determined as specific to HT‐rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia‐lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co‐expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant‐galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites. Significance Statement This study provides a significant chromosomal‐level genome assembly of Rhus chinensis, revealing evolutionary characteristics facilitating its adaptation to galling insects (Schlechtendalia chinensis). The findings reveal unique functional differentiation of tandem repeat clusters contributing to high gallotannin accumulation within S. chinensis‐induced gallnuts. The genome and the identified genes involved in this process provide invaluable genomic resources for further research.