The First Complete Chloroplast Genome of Lycium shawii: Genomic Architecture, Molecular Phylogenetics and...

Lycium shawii Roem. & Schult., a stress-resilient medicinal plant native to the deserts of Saudi Arabia, possesses notable bioactive compounds used in traditional medicine for treating inflammation, oxidative stress, and other ailments. However, its chloroplast (Cp) genome has not previously been sequenced or described, limiting accurate molecular identification and phylogenetic resolution. In this study, we present the first complete Cp genome of L. shawii. The plastome spans 155,936 bp and is organized into a large single-copy (LSC) region (86,608 bp), a small single-copy (SSC) region (18,430 bp), and two inverted repeats regions (IRA and IRB), each spanning 25,449 bp. A total of 128 genes were annotated, comprising 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Comparative genomic analyses revealed conservation of genome structure without major rearrangements across Solanaceae. Forty simple sequence repeats (SSRs) and 50 oligonucleotide repeats were identified, with mononucleotides (38) as the dominant SSR type, and forward repeats as the most common among longer repeats. RNA-editing sites were unevenly distributed, with the highest proportion in the LSC region (48%), followed by the SSC (29%) and IRs (23%). Nucleotide diversity analysis highlighted atpI, rbcL, and accD within the LSC region as hypervariable loci suitable for DNA barcoding. Plastome-wide phylogenetic reconstruction confirmed the placement of L. shawii within the tribe Lycieae of the subfamily Solanoideae. Molecular dating analysis suggested its emergence around 1.40 MYA, during the Calabrian stage of the Cenozoic era. This study provides the first Cp genome resource for L. shawii, offering new perspectives for evolutionary and comparative genomics within Solanaceae.