Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

Abstract

Background Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species. Results The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae. Conclusion All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.

The complete chloroplast genome of Ziziphus mairei Dode 1908 (Rhamnaceae), an endangered perennial plant in Yunnan, China

“…The previous studies of Ziziphus showed that eight species of Ziziphus formed a stable monophylete, our results of phylogenetic analysis are consistent with this (Asaf et al. 2022 ).…”

“… 2017 ), Z. hajarensis MZ475300 (Asaf et al. 2022 ), Ziziphus attopensis MW201670 (Li 2021 ), Ziziphus mauritiana KY628304 (Huang et al. 2017 ), Ziziphus spina-christ KY628305 (Huang et al.…”

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

“…T. hamiensis var. qatarensis and T. simplex plastomes are almost similar in size to previously reported Tetraena and Zygophyllum plastomes 56 and significantly shorter than other angiosperms 57 – 59 . Both Tetraena plastomes had a quadripartite structure, standard in vascular plants 60 , and the GC content was similar to that of many other angiosperm species 59 , 61 .…”

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

“…Genetic variations in G. mangostana cultivars have been shown by randomly amplified DNA fingerprinting (RAF) and inter simple sequence repeat (ISSR) molecular markers [ 58 , 59 , 60 ]. Plastomes also contain SSR and long repeats [ 61 , 62 , 63 , 64 ]. SSR, which is a stretch of 1–6 bp small repeats, is found extensively in different regions of the plastome, such as the intergenic regions, intron regions, and protein-coding regions [ 24 ].…”