Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

Abstract

Background Salvadora persica L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie’s cp genomes from the order Brassicales. Results The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. Conclusion The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

“…The codon usage among the four plastomes of Renanthera was consistent across the four species; the CDSs of the four species of Renanthera had the same preferences in codon usage for all 20 amino acids, indicating that the nucleotide sequences in the CDS of the four species were identical, which is deemed accurate. This is because plastome sequences of closely related species have greater conservatism as they were inherited from their most recent common ancestor ( Khan et al, 2021 ). Among these amino acids, leucine ( n = 19,700) is the most frequently used, cysteine ( n = 4,422) is the least universal amino acid in the cp genomes of these species.…”

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

“…It has a much lower substitution rate than a nucleic genome, and the substitution rate is even lower in two inverted repeat regions 33 . Noteworthy, information included in chloroplast genomes, as well as their almost nonrecombinant traits 34 , maternal transmission 35 , have made the chloroplast genome a good source for searching for clues about the origins of populations as well as for phylogenetic reconstructions, thereby clearing the ambiguities present in the evolutionary relationships 36 . Hence, today's strategies for discovering plant molecular phylogeny rely profoundly on cp genome sequences.…”

The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence

“…Diploid (AA), Tetraploid (AB, AG) and hexaploid (ABD, AGA m ) Triticum species plastomes showed conserved gene content and commonly harbored an identical set of annotated unique genes. These plastomes comprised 72–89 protein-coding genes, 4–8 rRNA genes, and 32–42 tRNA genes ( Table 1 ), which are characteristic of plastomes [ 60 , 61 , 62 , 63 ]. The number of genes annotated in plastomes ranged from 112 ( T. macha and T. monococcum subs monococcum ) to 136 ( T. turgidum subsp.…”