Characterization and comparative genomic analyses of complete chloroplast genome on Trema orientalis L.

Abstract

This study, T. orientaliswas used as an example to explore chloroplast genome evolution and determine Cannabaceae's phylogenetic relationship using phylogenetic analysis. Comparing six Trema species chloroplast genomes shows that gene order, gene content, and length are highly conserved yet dynamically evolve among species. The whole T. orientalis chloroplast genome is 157,134 bp long with accession number OQ871457 and includes a pair of inverted repeats (IRs) of 25,493 bp separated by a small single-copy region of 19,320 bp and a large single-copy region of 86,822 bp. The total content of GC is 36.3%. The chloroplast genome was annotated to include 129 genes, 84 of which code for proteins, 37 for tRNA, and 8 for rRNA. 127 SSRs were found, with the highest concentration in p1 (60), whose length varied from 10 to 16 bp; these areas could serve as foundational molecular markers for the Trema genus. The IRS repeats were found: 17 were forward repeats (F), 25 were palindromic repeats (P), and ve were reverse repetitions (R). T. orientalis and T. orientalis (NC _039734.1), with 99 percent similarity, were found in the same group in a phylogenetic analysis of Trema species. IR scope expansion and contraction were also determined and compared with 17 related species in this family. It is the rst report of the chloroplast genome of T. orientalis collected from Western Desert, Saudi Arabia, providing an important data reference for future investigations into genetic diversity and plant evolution. Such information based on the complete chloroplast genomes facilitates the evolution of species-speci c molecular tools to discriminate T. orientalis. Highlight 1. Study a detailed analysis of the entire chloroplast genome of Trema orientalis, offering a comprehensive understanding of its genetic structure.2. The study compares the chloroplast genome of Trema orientalis with those of other plant species, facilitating a comparative analysis that sheds light on the evolutionary relationships and divergence patterns in this plant.3. Identify the genes present in the chloroplast genome of Trema orientalis and analyze their arrangement. This information helps in deciphering the functional roles of different genes and their potential contributions to the plant's physiology.4. Provides insights into the evolutionary history of Trema orientalis. It contributes to our understanding of the adaptive changes that have occurred within this plant species over time.5. The characterization and comparative analysis of the Trema orientalis chloroplast genome have implications for conservation efforts and phylogenetic research. This information can aid in the development of conservation strategies and contribute to the taxonomy and classi cation of related plant species.