The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of Garcinia paucinervis

Abstract

Garcinia paucinervis is an evergreen tree with high medicinal value. Due to its vulnerable reproductive capacity coupled with excessive logging by humans, G. paucinervis has become an endangered species. In order to protect this species effectively, we drew the complete chloroplast genome of G. paucinervis and performed a series of comparative analyses on G. paucinervis and its neighbouring species. The chloroplast genome size of G. paucinervis is 157702 bp. In the chloroplast genome, we identified 130 genes, 56 RNA editing sites in the protein-coding genes, as well as 241 simple sequence repeats (SSRs) and 49 complex repetitive sequences. Comparative analysis identified some high divergent sequences in the intergenic spacers, which can be used as candidate markers for phylogenetic study. From an adaptive evolution point of view, a branch-site model analysis identified positively selected sites in 5 genes, most of which are involved in ribosome biogenesis, protein synthesis and other developmental processes. The detected codon substitutions may be associated with the evolution of G. paucinervis to adapt to the extreme habitat in karst. In addition, the result of the phylogenetic analysis supports the previous phylogenomic studies of taxa within the rosids clade. The ML tree revealed that G. mangostana was a sister to G. gummi-gutta, and they formed a diverging lineage to G. paucinervis in Garcinia. The above information is of great significance for us to understand the evolution of G. paucinervis chloroplast and lays the foundations for future studies in species conservation.

Keywords:

• Garcinia paucinervis
• chloroplast genome
• phylogenetic analysis
• adaptive evolution

Acknowledgements

We are sincerely grateful to Yusong Huang (Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China) for providing plant picture.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The data generated during this study is available at Genbank (accession number: MT501656)

Additional information

Funding

This work was supported by the National Science Foundation of China (31960276), the National Science Foundation of Guangxi (2018GXNSFAA281015), and the Guilin Medical University Start-up fund (20501019034).