Chloroplast Genome Analysis of Six Camellia sinensis Accessions: Genetic Divergence, Adaptive Evolution, and Molecular Marker Development

<i>Camellia sinensis</i> 'hainanensis' (Hainan Sheng tea) is an endemic tea germplasm resource native to Hainan Island, China. Using complete chloroplast genome sequencing combined with comprehensive comparative analyses, we elucidated the genetic architecture of six <i>C. sinensis</i> accessions. The chloroplast genomes exhibited a typical quadripartite circular structure (~157 Kb) comprising 80 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Expansion and contraction of the inverted repeat (IR) regions led to boundary shifts affecting genes, while nucleotide diversity within the large single-copy (LSC) and small single-copy (SSC) regions (Pi > 0.0035) markedly exceeded that of the conserved IR regions. Phylogenetic reconstruction revealed that <i>C. sinensis</i> 'hainanensis' shared the closest evolutionary relationship with Yunnan large-leaf tea (<i>Camellia grandibracteata</i>), supporting its independent lineage within the genus. A polymorphic molecular marker derived from the hypervariable non-coding region (<i>trnT-psbD</i>) may serve as a useful preliminary marker for distinguishing <i>C. sinensis</i> 'hainanensis' from related taxa and hybrids. This study provides the first comprehensive comparison of complete chloroplast genomes of six <i>C. sinensis</i> 'hainanensis', identifies three distinct plastome types, and develops a molecular marker that can reliably distinguish these types, offering valuable genomic resources for future studies on tea evolution and germplasm identification.