Widespread inspection and comparative analysis of ITS secondary structure conservation and covariation of Coccinellidae
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ORIGINAL RESEARCH ARTICLE
Widespread inspection and comparative analysis of ITS secondary structure conservation and covariation of Coccinellidae Chandni Verma 1 & Geetanjali Mishra 1 & Omkar 1 Received: 27 April 2019 / Accepted: 8 January 2020 # African Association of Insect Scientists 2020
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. Keywords Conservation . Covariation . ITS1 and ITS2 . Ladybirds . Secondary structure phylogenetic analysis
Introduction Coccinellidae, family of small predator beetles, display outrageous diversity. These beneficent insects play a promising role in pest management thus they are known as biocontrol agents. (Majerus et al. 1989; Dixon and Dixon 2000; Hodek and Honek 2013). Conventional methods i.e. phenotypic, behavioural and morphological traits were considered for phylogenetic classification of Coccinellidae subfamilies (Kovar 1996). However, it is difficult to distinguish closely related species, because they have very minute morphological variations (Pompeo et al. 2017). Thus, molecular and computational approaches, provide an appropriate overview of the genetic Electronic supplementary material The online version of this article (https://doi.org/10.1007/s42690-020-00105-y) contains supplementary material, which is available to authorized users. * Omkar [email protected] 1
Department of Zoology, Ladybird Research Laboratory, University of Lucknow, Lucknow 226007, India
composition to understand variations at the molecular level, helping to correlate the morphology variations and genetic composition. As studies attributed that internal transcribed spacers (ITS) molecular marke
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