First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees

Abstract

Commiphora gileadensis and C. foliacea (family Burseraceae) are pantropical in nature and known for producing fragrant resin (myrrh). Both the tree species are economically and medicinally important however, least genomic understanding is available for this genus. Herein, we report the complete chloroplast genome sequences of C. gileadensis and C. foliacea and comparative analysis with related species (C. wightii and Boswellia sacra). A modified chloroplast DNA extraction method was adopted, followed with next generation sequencing, detailed bioinformatics and PCR analyses. The results revealed that the cp genome sizes of C. gileadensis and C. foliacea, are 160,268 and 160,249 bp, respectively, with classic quadripartite structures that comprises of inverted repeat’s pair. Overall, the organization of these cp genomes, GC contents, gene order, and codon usage were comparable to other cp genomes in angiosperm. Approximately, 198 and 175 perfect simple sequence repeats were detected in C. gileadensis and C. foliacea genomes, respectively. Similarly, 30 and 25 palindromic, 15 and 25 forward, and 20 and 25 tandem repeats were determined in both the cp genomes, respectively. Comparison of these complete cp genomes with C. wightii and B. sacra revealed significant sequence resemblance and comparatively highest deviation in intergenic spacers. The phylo-genomic comparison showed that C. gileadensis and C. foliacea form a single clade with previously reported C. wightii and B. sacra from family Burseraceae. Current study reports for the first time the cp genomics of species from Commiphora, which could be helpful in understanding genetic diversity and phylogeny of this myrrh producing species.

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

“…There was a 186 bp difference observed between the two sequenced chloroplast genomes, and the size was also comparable with other compared Euphorbia species, as well as the Vernicia fordii chloroplast genome, which is 161,528 bp in length [32], suggesting that chloroplast genomes are conserved. The result was consistent with previously reported studies [30]. The total number of genes presented in the chloroplast genome is divided into three main categories.…”

“…However, it is similar to the previously reported B. sacra cp genome [42]. Among the dinucleotide SSRs, AT was found to be the most abundant in the sequenced and compared cp genomes, similar to the previously reported genomes [30]. Another and important characteristic of the chloroplast genome, which is useful for evolutionary studies, is the location of the boundaries among the four chloroplast regions.…”

“…The two sequenced cp genomes are comparatively analyzed with another cp genome to study the various parameters of these genomes. The chloroplast genome structure and gene order of these two chloroplast genomes are highly conserved with no specific genome inversion reported, and the gene order was the same and found consistent with previously reported genomes [30]. In the present study, we compared eleven chloroplast genomes.…”

“…The number of repeats, including forward, tandem, and palindromic repeats, were studied in the chloroplast genomes sequenced and compared, and were found in a larger amount than in the previously reported cp genome of V. fordii (49 repeats) [32]. Among these repeats, tandem repeats were found several times more than palindromic and forward repeats, which are consistent with the Teucrium and Commiphora species [30,31], as well as S. miltiorrhiza [39], as previously reported.…”

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

“…Automated gene-by-gene alignment ensures that any insertion or deletion at the 5' or 3' ends of a coding region does not result in an overlap of different genes in the resulting multi-gene alignment, which would not be the case when aligning the genes after their concatenation. (b) In the present investigation, the DNA sequences were aligned based on their amino acid, not on their nucleotide sequences, which some contemporary plastid phylogenomic studies continue to do (e.g., [68,69]). Conducting the alignment on amino acid instead of nucleotide sequences ensures that the trinucleotide reading frame of codons is preserved and, thus, insertions/deletions are always a multiple of three.…”