Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Abstract

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635–85,765 bp and a small single-copy (SSC) region of 18,457–18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.

Comparative genome analysis revealed gene inversions, boundary expansions and contractions, and gene loss in the Stemona sessilifolia (Miq.) Miq. chloroplast genome

“…The GC content decreased markedly from the first position to the third position in the codon position scale. Such a result was in line with the phenomenon observed in most land plant plastomes [42][43][44].…”

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis

“…The overall GC content is 37.60%, while the corresponding value in the LSC, SSC, and IR regions is 35.61%, 31.40%, and 42.99%, respectively ( Figure 1 ). As reported in other angiosperm (Mehmood et al 2019 , 2020a , b ; Su et al 2019 , 2021 ), the IR regions have the highest GC content due to the presence of rRNAs containing high GC content. Analysis of boundaries between the IRs and single copy regions of H. ginfushanicum find that the rps19 gene is 17 bp away from the LSC/IRb junction; The ndhF crosses the IRb/SSC boundary with a length of 29 bp in IRb and 2,182 bp in SSC and the ycf1 gene spans the SSC/IRa boundary with a length of 890 bp in SSC which results in a pseudogene ( ψycf1 ) at the IRa/SSC border ( Figure 2 ).…”

Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

“…Plant photosynthesis is strictly controlled by heredity, so understanding the gene function and phylogenetic relationships of cp genomes is critical to understanding the origin and evolution of organelles, and has applications in crop improvement and enhancing photosynthetic efficiency ( Zhao et al, 2019 ). The cp genome is mostly a quadripartite structure comprising one large single-copy region (LSC), one small single-copy region (SSC), and two reverse repeats ( Abdullah et al, 2019a ; Mehmood et al, 2020 ). However, linear cp genomes have been reported ( Oldenburg and Bendich, 2015 ).…”