Chromosome-level genome assembly and resequencing of camphor tree (<i>Cinnamomum camphora</i>) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of <i>Cinnamomum</i>

Abstract

<i>Cinnamomum</i> species attract attentions owing to their scents, medicinal properties, and ambiguous relationship in the phylogenetic tree. Here, we report a high-quality genome assembly of <i>Cinnamomum camphora</i>, based on which two whole-genome duplication (WGD) events were detected in the <i>C. camphora</i> genome: one was shared with Magnoliales, and the other was unique to Lauraceae. Phylogenetic analyses illustrated that Lauraceae species formed a compact sister clade to the eudicots. We then performed whole-genome resequencing on 24 <i>Cinnamomum</i> species native to China, and the results showed that the topology of <i>Cinnamomum</i> species was not entirely consistent with morphological classification. The rise and molecular basis of chemodiversity in <i>Cinnamomum</i> were also fascinating issues. In this study, six chemotypes were classified and six main terpenoids were identified as major contributors of chemodiversity in <i>C. camphora</i> by the principal component analysis. Through <i>in vitro</i> assays and subcellular localization analyses, we identified two key terpene synthase (TPS) genes (<i>CcTPS16</i> and <i>CcTPS54</i>), the products of which were characterized to catalyze the biosynthesis of two uppermost volatiles (i.e. 1,8-cineole and (iso)nerolidol), respectively, and meditate the generation of two chemotypes by transcriptional regulation and compartmentalization. Additionally, the pathway of medium-chain triglyceride (MCT) biosynthesis in Lauraceae was investigated for the first time. Synteny analysis suggested that the divergent synthesis of MCT and long-chain triglyceride (LCT) in Lauraceae kernels was probably controlled by specific medium-chain fatty acyl-ACP thioesterase (FatB), type-B lysophosphatidic acid acyltransferase (type-B LPAAT), and diacylglycerol acyltransferase 2b (DGAT 2b) isoforms during co-evolution with retentions or deletions in the genome.