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Widespread inspection and comparative analysis of ITS secondary structure conservation and covariation of Coccinellidae

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Abstract

ITS1 and ITS2 of ribosomal DNA (rDNA) of six subfamilies i.e. Epilachaninae, Chilocorinae, Coccinellinae, Coccidulinae, Scymininae Ortaliinae and Sticholotidinae were examined, aligned and conserved motifs in folding patterns of stable consensus secondary structures were assessed. RNAalifold and RNA fold algorithms applied by RNAz program to compute consensus secondary structures and MFE efficiently and derive a number of statistical scores i.e. SCI, Z-score and MPI. Assembled subsets in ITS1 (three sets) and ITS2 (ten sets) were significantly conserved. In this study, analysis of these consensus secondary structures shows that a motif sequence is remain conserved in all the species. Helices in subsets of ITS1 showed compensatory base involvement to maintain the stability and conservation of secondary structures during natural selection. Secondary structures of ITS2 found more conserved than ITS1. MP, BI and ML methods used to establish the evolutionary relationship, compared the topology significance on the basis of SCI and MPI in defined sets. Coccinellinae, Epilachaninae and Scymninae (all strains of species) were monophyletic whereas Coccidulinae, and Chilocorinae had inadequate sequence information. Of Ortaliinae and Sticholotidinae, yet no ITS sequences have been submitted. Thus, analysis of the structural folding patterns of ITS regions provided further prime information of species relatedness and inter-intra-specific variations.

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Acknowledgements

CV gratefully acknowledges UGC-NFSC Fellowship by University Grant Commission, New Delhi, India (F1-17.1/2017-18/RGNF-2017-18-SC-UTT-30386 dated July 15, 2017.

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  1. Department of Zoology, Ladybird Research Laboratory, University of Lucknow, Lucknow, 226007, India

    Chandni Verma, Geetanjali Mishra &  Omkar

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  1. Chandni Verma
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Verma, C., Mishra, G. & Omkar Widespread inspection and comparative analysis of ITS secondary structure conservation and covariation of Coccinellidae. Int J Trop Insect Sci 40, 587–597 (2020). https://doi.org/10.1007/s42690-020-00105-y

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