Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales

Abstract

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-021-01051-w.

Keywords: Chloroplast genome; Evolvulus alsinoides; Genes; Purifying selection; Simple sequence repeats.

Fig. 1

cp genome map of E. alsinoides. Genes in the inner circle are transcribed clockwise, and genes in the outer circles are transcribed in counter-clockwise direction. The IR/LSC/SSC boundaries are represented in the inner circle. The inner grey circle represent the GC and AT content of the cp genome

Fig. 2

A Number of SSRs in cp genome, coding region and non-coding region. B Frequency of SSR motifs in the cp genome. The X-axis represent the type of repeats and the Y-axis represents the No of SSRs

Fig. 3

Comparison of SSRs with the closely related species of E. alsinoides

Fig. 4

Representative agarose gel image of SSR amplified regions in E. alsinoides. Gel image showing amplification with 3% agarose. Lane1 represents 1 kb DNA ladder and Lane2 to 14 represents SSR1 to SSR13

Fig. 5

Comparison of cp genomes of five species within the family Convolvulaceae with reference to the cp genome of E. alsinoides. The name of the genes, their position and orientation are shown above the alignment. X-axis shows the cp genome coordinates while Y-scale shows percent identity between 50 and 100%

Fig. 6

Cp genome comparison of LSC, IRb, SSC and IRa border region of E. alsinoides with five species belongs to the family Convolvulaceae

Fig. 7

Comparison of nonsynonymous (Ka) and synonymous (Ks) substitution rates among eighteen species of Solanales. Protein-coding genes name is shown in X-axis, and the mean Ka/Ks values are shown in Y-axis

Fig. 8

Nuclear diversity (Pi) analysis of eighteen species of the order Solanales. The X-axis denotes the midpoint position of the window while the Y-axis denotes nucleotide diversity (Pi) of window. The thick blue line specifies the threshold for variation hotspots (Pi threshold = 0.13). The highly variable regions are represented in the graph

Fig. 9

Phylogenetic tree of complete cp genome constructed using BI, ML and MP methods. The values above the nodes are Bayesian posterior probabilities, MP and ML bootstrap values. The values inside the clades represent the divergence times and the divergence dates in Mya are represented in the nodes