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

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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.

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Abbreviations

AA:

Amino Acid

Cp:

Chloroplast

IR:

Inverted repeat

LSC:

Large Single Copy

PCGs:

Protein Coding Genes

RSCU:

Relative Synonymous Codon Usage

SMRT:

Single Molecule Real Time

SSC:

Small Single Copy

SSR:

Simple Sequence Repeat

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Acknowledgements

Our sincere gratitude to Prof. P. R. Sudhakaran and Prof. Oommen V Oommen for their valuable suggestions. The support provided by Mr. Deelip Kumar R., Campus Computing Facility (CCF), University of Kerala is gratefully acknowledged. We are grateful to the Campus Computing Facility (CCF) at the Central Laboratory for Instrumentation and Facilitation, University of Kerala for providing the HPC/GPU cluster facility to carry out this research work. We thank AgriGenome Labs, Cochin, Kerala, India, for performing Illumina sequencing.

Funding

We acknowledge the funds received from the University of Kerala (Plan fund) and also the facility under SIUCEB project, DBT –BIF centre, MHRD-FAST (AiCADD center) in the Department of Computational Biology and Bioinformatics, University of Kerala.

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  1. Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India

    P. R. Shidhi, V. C. Biju, Sheethal Vijayan, Anu Sasi, C. L. Vipin, Akhil Janardhanan, S. Aswathy, Veena S. Rajan & Achuthsankar S. Nair

  2. Department of Biotechnology, Inter University Centre for Genomics and Gene Technology, University of Kerala, Thiruvananthapuram, Kerala, India

    F. Nadiya

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Contributions

SPR and ASN designed the study. SPR, VCB, SV, AS, VCL, VR, AJ and AS conducted the experiments and performed the analysis. NF conducted the experimental validation of SSR. SPR coordinated the project and wrote the manuscript.

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Correspondence to P. R. Shidhi.

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Shidhi, P.R., Nadiya, F., Biju, V.C. et al. Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales. Physiol Mol Biol Plants 27, 1867–1884 (2021). https://doi.org/10.1007/s12298-021-01051-w

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