# Complete Chloroplast Genome Sequence of the Endemic and Medicinal Plant Zingiber salarkhanii: Comparative Analysis and Phylogenetic Relationships

## TL;DR

This study sequenced the chloroplast genome of Zingiber salarkhanii, a medicinal plant found only in Bangladesh, and compared it to other ginger family species to better understand its evolutionary relationships.

## Contribution

The first complete chloroplast genome of Zingiber salarkhanii is reported, offering insights into its phylogeny and genomic features.

## Key findings

- The chloroplast genome of Zingiber salarkhanii is 163,980 bp and contains 138 genes in a typical quadripartite structure.
- The species is most closely related to Zingiber recurvatum within the core Zingiber lineage.
- The study identified 211 SSRs and 11 mutation hotspots, useful for future species identification and comparative studies.

## Abstract

Zingiber salarkhanii is a plant found only in Bangladesh, and until now, its genetic information was largely unknown. In this study, we analyzed its complete chloroplast DNA to learn more about its identity and how it relates to other members of the ginger family. The circular genome measures 163,980 bp and contains 138 genes arranged in the typical quadripartite structure. Our findings show that it is closely linked to other Zingiber species and shares many traits common to this group. We also identified simple sequence repeats (SSRs) and variable hotspot regions that could be useful for future species identification and comparative studies. The plant is recognized for its attractive pink flowers and large fruit, and previous botanical studies have noted the presence of natural compounds of potential medicinal value. This work provides the first plastome resource for Z. salarkhanii, offering important information for taxonomic clarification, evolutionary assessment, and conservation planning. We also highlight the need to study additional Zingiber species to build a clearer understanding of their diversity and relationships within the ginger family.

Zingiber salarkhanii (Zingiberaceae family) is an endemic species of Bangladesh. It possesses biological effects, including analgesic, anxiolytic, cytotoxic, and antioxidant properties. Although genomic data on Zingiber is scarce, the entire chloroplast (cp) genome has been extensively used as a molecular marker to resolve phylogenetic issues. The genome size is 163,980 bp, and it has a standard quadripartite structure, with an average GC content of 36.91%. The genome contains 138 genes (113 unique), comprising 90 protein-coding genes, 79 unique genes, 48 noncoding genes (34 unique), 40 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). Codon usage analysis of the cp revealed 14 high-frequency codons besides 18 optimal codons in this species. A repetitive study revealed 211 simple sequence repeats (SSRs), predominantly A/T mononucleotide repeats. Sequence alignment indicated that variable regions were primarily located in the single-copy regions. Sequence comparison showed that most variable regions were located within the single-copy regions, and nucleotide diversity (π = 0–0.11289) indicated overall low divergence with 11 mutation hotspots. Phylogenetic investigations using both coding sequences and complete cp genomes indicated that Z. salarkhanii is most closely related to the Zingiber genus. Phylogenetic investigations using both coding genes and complete cp genomes placed Z. salarkhanii within the core Zingiber lineage, revealing its closest relationship to Z. recurvatum rather than to the genus. It conducted an extensive analysis of many cp genomic characteristics for phylogenetic significance, including overall genome architecture, codon usage bias, repetitive sequences, inverted repeat borders, and phylogenetic reconstruction. These findings provide a basis for further research to elucidate the molecular evolutionary dynamics of individual population variability within the species and genus. The plastome reported here also provides an essential genomic reference for future work on population variation and species differentiation within Zingiber.