In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis

SUMMARY Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health‐related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple‐leaved assamica cultivar “Zijuan”, the temperature‐sensitive sinensis cultivar “Anjibaicha” and the wild accession “L618” whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene‐centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene‐centric variants, especially for Anthocyanidin synthases. We constructed a gene‐centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes. Significance Statement Pangenomes aim to address the presence‐absence and copy number variation as well as structural variation within species for improved genomic analyses. A new pan‐genome, constructed from de novo genome assemblies of three diverse tea accessions, was merged with eight existing accessions using a novel, consistent gene and transposon annotation to provide a consistent resource and show differences in the catechin pathway.