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

• Published in: Genetic resources and crop evolution 2024-03, Vol.71 (3), p.1085-1099
• Main Authors: Ibrahim, Amira A., Alwutayd, Khairiah Mubarak, Safhi, Fatmah Ahmed, Alshegaihi, Rana M., Alqurashi, Mohammed, Alyamani, Amal, Aloufi, Salman, Alharthi, Badr, Fayad, Eman, Abd El-Moneim, Diaa
• Format: Article
• Language: English
• Subjects: Agriculture; Biomedical and Life Sciences; chloroplast genome; Chloroplasts; Completeness; Evolution; family; Gene order; genes; Genetic diversity; genetic variation; Genomes; Genomic analysis; genomics; genus; Life Sciences; Phylogenetics; Phylogeny; Plant Genetics and Genomics; Plant Physiology; Plant Sciences; Plant Systematics/Taxonomy/Biogeography; Research Article; rRNA; Saudi Arabia; Species; Trema; tRNA
• ISSN: 0925-9864; 1573-5109
• DOI: 10.1007/s10722-023-01678-6

In this study, Trema orientalis was 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. Regarding, there are 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 five were reverse repetitions (R). T. orientalis and T. orientalis (NC_039734.1), with 99% 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 first 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-specific molecular tools to discriminate T. orientalis.