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 their maternal lineages and adaptive evolution is still limited. The genetic relationship of the populations in Tingping Township (Chengbu County) has always 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 with nine other accessions, we built a robust dataset of 15 samples that better represents the broader area of Shaoyang. These plastomes range in size from 156,697 to 157,098 bp and have the typical quadripartite structure. However, research on the dynamics of inverted repeats (IR) has found that there are three different structural architectures - standard, IR-contraction, and wild specialisation - suggesting that its evolutionary path may be more complex than initially thought. In addition to the five mutation hotspots (trnC-petN, ycf1, etc.), it has been found that there is a case of positive selection in genes such as ndhB and rpoC1, which may be adapted to local environmental stresses. In particular, our phylogeny also exhibits a significant "West Large vs East Small" leaf type division. The Tingping samples display a mosaic maternal ancestry comprising both var. assamica and var. sinensis chloroplast lineages, suggesting differential seed-mediated gene flow during the domestication history of this region.Conclusions This study provides the map of the maternal genetic structure of Shaoyang tea plants. The discovery of complex introgression events 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.