# Complete chloroplast genome sequence of Pachystachys lutea Nees: genome structure, adaptive evolution, and phylogenetic relationships

## TL;DR

This paper reports the complete chloroplast genome of Pachystachys lutea, revealing its structure, evolution, and phylogenetic relationships with other plants.

## Contribution

The study is the first to report the complete chloroplast genome and phylogenetic analysis of the genus Pachystachys.

## Key findings

- The chloroplast genome of P. lutea has a typical quadripartite structure with 132 annotated genes.
- Genes like rps19, ycf1, and ndhF show high nucleotide polymorphism and may aid in molecular identification.
- Phylogenetic analysis shows P. lutea forms a sister group with Clinacanthus nutans with 100% bootstrap support.

## Abstract

Pachystachys lutea Nees is a typical species of the family Acanthaceae, native to tropical South America. As an evergreen shrub, it has found extensive application in landscape greening due to its unique ornamental value. However, there are currently no phylogenetic and genetic studies on the chloroplast (cp.) genome of P. lutea.

This study characterized the cp. genome of P. lutea using high-throughput sequencing technology and analyzed its structural features and phylogenetic position using bioinformatics methods. The results indicated that the cp. genome had a high degree of conservation in gene structure and gene content, with a typical quadripartite structure. Its total length is 151,574 bp and the total GC content is 38.18%. A total of 132 genes were annotated, including 87 protein-coding genes (PCGs), 37 tRNAs and eight rRNA genes. Through the comparative analysis, the diversity and variation of large single-copy (LSC) and small single-copy (SSC) regions were significantly higher than those of inverted repeat (IR) regions. Genes with high nucleotide polymorphism, such as rps19, ycf1, and ndhF provided potential reference loci for molecular identification within the P. lutea. The phylogenetic analysis showed that the P. lutea and Clinacanthus nutans forms a sister group with 100% bootstrap value, which proves that P. lutea develops conservatively in the course of evolution.

This paper for the first time reports the phylogenetic study of the complete cp. genome within the genus Pachystachys. The study provides a theoretical basis for the research on genetic diversity, molecular markers, and species identification of plants in the Acanthaceae family. It enriches the genetic information and supports the evolutionary relationships among plants in this family.

The online version contains supplementary material available at 10.1186/s12863-025-01380-9.