The Cannabaceae family has ten genera and about 117 species (Sytsma et al. 2002; Bell et al. 2010; Byng et al. 2016). The Cannabaceae family consists primarily of woody plants. However, it does include at least one herb (Cannabis L.) and a few vines (Humulus L.). The family is found worldwide in both tropical and temperate climates. Species such as Aphananthe (Thunb.) Planch., Celtis L., and Trema Lour (Yang et al., 2013). Trema orientalis L. is a tree in the Cannabaceae family with leaves that stay green all year. The height of this tree changes depending on the weather and where it grows. There is a tendency for the leaf base to be different lengths and widths. The length can range from 2 to 20 cm, and the width from 1.2 to 7.2 cm. Even though the flowers are small, green, and not very noticeable, they are carried in dense bunches that are short and close together. The small fruits are round, dark green or purple, and turn black when ready; they are carried on very short stalks (Farzana et al., 2022). This plant has strong roots that help it stay alive during long periods of drought (Adinortey et al., 2013). Some common names for the plant are pigeon wood, hop out, charcoal tree, Indian charcoal tree, Indian nettle tree, and gunpowder tree. This tree species can be found worldwide (Orwa et al., 2009), and it can grow in different climate zones and soil types, from heavy clay to light sand (Smith, 1966). T. orientalis is a potentially versatile animal feed. Nonetheless, the adequate seed remains a significant obstacle for most fodder promotion attempts (Franzel et al. 2014). The seeds of T. orientalis are gathered from the wild, where populations have diminished in part due to the destruction of natural habitats and may also have a significant role in determining the distribution of pioneer species like T. orientalis (Goodale et al., 2014). Hence, stochastic alterations in the genetic integrity of the seeds of this promising fodder species in the wild are expected to occur (Schippmann et al., 2002; Nantongo and Gwali, 2018). Determining the genetic structure of T. orientalis can aid in developing conservation, management, and sustainable use strategies (Frankham et al., 2002; Nantongo et al., 2016; Coates et al., 2018; Nantongo et al., 2020).
In addition to being used to make paper and poles, it has also been used in traditional medicine. Almost every part of the plant is used as medicine to treat infections in tropical areas, diseases caused by worms, and lung inflammation (Nkansa-Kyeremateng, 1992; Adinortey et al., 2013). Even though they are important for medicine, not much has been written about them recently (Al-Robai et al., 2022), and there aren't many genomic resources that can help improve and domesticate them. T. orientalis is often employed as a natural pioneer in conventional medicine to treat illnesses (Adinortey et al., 2013). Fever reduction and infection prevention are two common uses for this species. Tremetol, simiarenol, and simiarenone are important phytochemical ingredients of T. orientalis leaves; tremetol, swertianin, scopoletin, and numerous fatty acids and glycosides are found in the stem bark; sterols and fatty acids are found in the roots (Parvez et al., 2019). Plants, algae, and cyanobacteria use chloroplast organelles to perform photosynthesis. Chloroplasts also perform several crucial metabolic roles. Many amino acids, lipids, pigments, and vitamins are among these. Starch is stored, and sugar is biosynthesized as well. Plants can't grow or develop without the energy provided by the nitrogen cycle and sulfate reduction (Neuhaus and Emes, 2000; Bausher et al., 2006; Richardson and Schnell, 2020). The chloroplast DNA is a typical double-stranded circular genome found in higher plants (Sugiura, 1995; Odintsova and Yurina, 2006; Ruhlman and Jansen, 2014; Iram et al., 2019). One large single-copy (LSC) region, one short single-copy (SSC) region, and two inverted repeats (IR) sections make up the normal chloroplast genome (Zhou et al., 2016). Because of their maternal inheritance, small genome size, and low mutation rate, chloroplasts' genomic information has been widely used to produce molecular markers for use in population genetics, genome evolution, phylogenetics, and constructing DNA barcoding markers (Sun et al., 2020; Guan et al. 2022; Feng et al., 2023).
As a result of their low nucleotide substitution rates, structural simplicity, and uniparental inheritance (Yang et al., 2019), chloroplast genomes are often used for species identification (Yu et al., 2021) and are excellent resources for phylogenetic investigations (Yang et al., 2019). Because of its consistent structure and wealth of genetic data may be used to investigate intricate evolutionary connections (Oldenburg and Bendich, 2016). Nonetheless, DNA barcoding uses some genes, such as rbcL and matK, to identify species positively; this gives molecular marker research hope (Hollingsworth, 2011). As chloroplast genomes carry more genetic information than gene fragments, they are used in studies of plant genetic diversity and conservation (Wariss et al., 2018). Chloroplast genome data is augmented by next-generation sequencing (NGS) technology, which assembles it swiftly and affordably (Tangphatsornruang et al. 2010). Thus, the current study sought to use next-generation sequencing technology to sequence, assemble, and describe the complete chloroplast genome sequences of a medicinal T. orientalis wild variant found in the Western Desert area and study the genomic relationships among T. orientalis and its related species. This information from the chloroplast genome paves the way for investigations into the phylogenetic evaluation, practical application, and conservation genetics of T. orientalis.