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Gene Expression Prediction and Hierarchical Clustering Analysis of Plant CCD genes

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Abstract

Plant carotenoid cleavage dioxygenase (CCD) catalyses the formation of industrially important apocarotenoids. Here, we applied codon-based classification for 72 CCD genes from 35 plant species using hierarchical clustering analysis. The codon adaptation index (CAI) and relative codon bias (RCB) were utilized to estimate the level of gene expression. The codon-based cluster tree result shows neatly clustered subclass of CCD genes except BoCCD1 gene of Bixa orellana. Correlation analysis of CAI values with RCB indicates an overall low-level expression of CCD across different species. Similarly, the closeness in the codon cluster with same CAI values was not reflected in 3-D structural report of selected CCD genes. These finding not only enhances our insights into the classification of CCD gene across the species but also identifies the critical factors responsible for this variation, which could aid in prediction of gene expression and function for newly reported CCD genes.

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Acknowledgments

We express our sincere gratitude to Science and Engineering Research Board–Department of Science and Technology, New Delhi, India, for the support extended through the project (SR/FT/LS-75/2011). The authors are grateful to VIT University management for their constant support.

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Authors and Affiliations

  1. School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India

    R. Priya, J. Febin Prabhu Dass & Ramamoorthy Siva

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  1. R. Priya
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  2. J. Febin Prabhu Dass
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  3. Ramamoorthy Siva
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Correspondence to Ramamoorthy Siva.

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Fig. S1

Hierarchical cluster tree based on ward’s method with CAI values (DOCX 37.8 kb)

Fig. S2

Hierarchical cluster tree based on average linkage method with CAI values (DOCX 38 kb)

Fig. S3

Hierarchical cluster tree based on complete linkage method with CAI values (DOCX 38.1 kb)

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Priya, R., Dass, J.F.P. & Siva, R. Gene Expression Prediction and Hierarchical Clustering Analysis of Plant CCD genes. Plant Mol Biol Rep 34, 618–627 (2016). https://doi.org/10.1007/s11105-015-0950-2

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