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

## TL;DR

Scientists analyzed the chloroplast genomes of six tea plant varieties from Hainan Island to understand their genetic differences and identify a unique DNA marker for one variety.

## Contribution

The study developed a molecular marker for distinguishing the Hainan tea variety and identified three distinct genetic types among the accessions.

## Key findings

- Three distinct plastome types were identified among six Camellia sinensis accessions.
- A polymorphic marker from the trnT–psbD region can distinguish C. sinensis ‘hainanensis’ from related taxa.
- Genetic divergence and adaptive evolution were observed in the chloroplast genomes of Hainan tea.

## Abstract

Scientists studied a special type of tea plant that is native to Hainan Island in China. Their aim was to understand its unique genetic blueprint in order to protect and make better use of this valuable plant. By analyzing the complete chloroplast genome, they compared six different tea accessions. They found that it could be grouped into three distinct genetic types. The researchers also discovered a tiny, specific difference in the DNA of one variety that acts like a unique fingerprint. This DNA fingerprint can be used to quickly and accurately distinguish this variety from others. This work provides a deeper understanding of the evolution of Hainan tea and offers a simple genetic tool for identifying it, which will be important for conserving this special variety and breeding improved plants in the future.

Camellia sinensis ‘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 C. sinensis 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 C. sinensis ‘hainanensis’ shared the closest evolutionary relationship with Yunnan large-leaf tea (Camellia grandibracteata), supporting its independent lineage within the genus. A polymorphic molecular marker derived from the hypervariable non-coding region (trnT–psbD) may serve as a useful preliminary marker for distinguishing C. sinensis ‘hainanensis’ from related taxa and hybrids. This study provides the first comprehensive comparison of complete chloroplast genomes of six C. sinensis ‘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.