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

Sajjad Asaf,Ahmed Al-Harrasi,Waqar Ahmad,Abdul Latif Khan

doi:10.1186/s12864-022-08320-2

Sajjad Asaf, Ahmed Al-Harrasi + Show 2 more

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https://doi.org/10.1186/s12864-022-08320-2

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Journal: BMC Genomics	Publication Date: Jan 27, 2022
Citations: 9	License type: open-access

Affiliation: University of Nizwa, University of Houston

Abstract

BackgroundZiziphus 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.ResultsThe 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.ConclusionAll 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.

Highlights

Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman
General features and Organization of Chloroplast Genome The chloroplast genome of the Z. hajarensis was 162,162 bp: among the largest found among the analyzed genomes
The cp genome of Z. hajarensis is a typical circular molecule organized in 4 parts, the two inverted repeats (IR) of 26,499 bp in size, contributing 16.34% to the genome size, that divides the rest of the genome sequences into a small single

Summary

Introduction

Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. We sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species. Is one of the medicinally and economically important genera of Family Rhamnaceae. It is disseminated across the sub-tropical and warm-climatic zones of the world. The members of the Ziziphus genus are shrubs (with thorns) and small trees, which vary in numbers as claimed by various reports, like 86 [1, 2], 135. The available genomic sequences are only of few member plants [8]; because of the diversity in views and limited genomic information available, the intra-generic classification is a difficult problem [9]. The relationship between Rhamnaceae and Elaeagnaceae has been established by studies using 18S nuclear ribosomal DNA, atpB, and rbcL sequence data [14, 15]

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