Comparative chloroplast genome analysis reveals genetic differentiation and maternal introgression in tea plants (Camellia sinensis) from Shaoyang, China

BACKGROUND: Although the tea germplasm resources in the Shaoyang area of south-west Hunan Province, China, are extremely diverse, knowledge of the maternal lineages and adaptive evolution of these resources is still limited. The genetic relationship of the populations in Tingping Township (Chengbu County) has long been a focus of attention, but due to insufficient genetic information, it was not determined to which branch they belonged in the phylogenetic tree. RESULTS: By integrating the newly sequenced chloroplast genomes of Tingping tea plants with nine other accessions, we built a robust dataset comprising 15 samples that representing the broader area of Shaoyang. These plastomes range in size from 156,697 to 157,098 bp and have the typical quadripartite structure. Comparative genomic analysis of these chloroplast genomes revealed high sequence conservation (90-100% identity) with no rearrangements or large indels, yet identified 19 hypervariable intergenic regions (e.g., trnH-psbA, trnC-petN, ndhF-rpl32) and five divergent protein-coding genes (rpoC2, ycf2, ndhB, ccsA, ndhE) concentrated in non-coding regions. Analysis of inverted repeat (IR) dynamics uncovered three distinct structural architectures-standard type, IR-contracted type, and wild-specialized type-suggesting a more complex evolutionary trajectory than initially assumed. Based on statistical analyses using the PAML branch-site model, chloroplast genes in the target clade were not subject to positive selection, further supporting the view that the chloroplast genome is highly conserved. Our phylogeny also reveals a significant "West Large vs East Small" leaf type division. The Tingping samples exhibit a mosaic maternal ancestry comprising both var. assamica and var. sinensis chloroplast lineages, indicating that this region has experienced complex historical gene flow, likely associated with cultivation and seed exchange. These chloroplast genome patterns are consistent with maternal lineage introgression (chloroplast capture), although nuclear markers would be required to confirm true introgression and to distinguish ancient divergence from recent admixture. CONCLUSIONS: This study provides the map of the maternal genetic structure of Shaoyang tea plants. The discovery of a distinct maternal lineage in 'zhuyedong' and complex patterns consistent with chloroplast capture in Tingping not only restructures our understanding of local tea evolution but also provides an indispensable genetic basis for the conservation of gene pools and the breeding of excellent tea varieties.