Complete chloroplast genome characterization and phylogenetic analysis of two natural caffeine-free Camellia yungkiangensis H. T. Chang accessions

The discovery and utilization of naturally caffeine-free tea germplasms hold significant potential for developing novel tea products tailored to health-conscious consumers. This study focuses on Camellia yungkiangensis , a rare caffeine-free tea plant resource, to systematically evaluate its biochemical traits, chloroplast genome architecture, and phylogenetic relationships. A total of 162 germplasm samples from five distinct populations in Guizhou, China, were analyzed for catechins and alkaloids. Results confirmed the universal absence of caffeine across all accessions, accompanied by high theobromine content (average 4%) and a unique catechins profile characterized by low epigallocatechin gallate (EGCG, <1%) and high catechin (C, >6%) levels. Two morphologically distinct types accessions—shrub (RJ) and tree (SD)—were selected for complete chloroplast genome sequencing utilizing the Oxford Nanopore sequencing platform. Both genomes exhibited a typical quadripartite structure, with total lengths of 156,872 bp (RJ) and 156,892 bp (SD), and encoded 133 identical genes. Repetitive sequence analysis identified 69 (RJ) and 70 (SD) SSRs, predominantly mononucleotide and dinucleotide repeats, and a unique hexameric SSR (AAAGAA) 3 present exclusively in RJ serves as a distinctive molecular marker. Phylogenetic reconstruction using 55 Camellia species placed RJ and SD in a distinct clade closely related to C. pitardii and C. danzaiensis , highlighting their evolutionary divergence from cultivated tea plant varieties. These findings provide genomic and biochemical foundations for leveraging C. yungkiangensis in breeding programs aimed at expanding the diversity of specialty teas, particularly caffeine-free varieties with unique health benefits.