Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales
Authors
P Shidhi
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
Veena Rajan
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
S Aswathy
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
Akhil Janardhanan
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
C Vipin
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
Anu Sasi
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
Sheethal Vijayan
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
V Biju
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
F Nadiya
Department of Biotechnology, Inter University Centre for Genomics and Gene Technology, University of Kerala, Thiruvananthapuram, Kerala India
Achuthsankar Nair
Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
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: Evolvulus alsinoides, Chloroplast genome, Genes, Simple sequence repeats, Purifying selection
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