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Sequence characteristics and phylogenetic implications of the nrDNA internal transcribed spacers (ITS) in the genus Nymphaea with focus on some Indian representatives

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Abstract

Nymphaea, an aquatic perennial herb with exceptionally beautiful flowers and floating leaves, is well represented globally. Out of ten species reported from India, the internal transcribed spacers (ITS) region of nrDNA was investigated in seven species of Nymphaea viz. N. alba var. rubra, N. caerulea, N. × marliacea, N. nouchali, N. pubescens, N. rubra and N. tetragona. Barring N. pubescens, whereby double peaks detected in the sequencing chromatograms may be due to random mutations occurring in some of the ITS paralogues, the additional signals detected for N. alba var. rubra and N. rubra are probably influenced by recent hybridization and introgression. Our study on sequence characteristics of ITS 1 and ITS 2 revealed high G + C content (ITS 1, 45.5–48.4%; ITS 2, 50.2–51.5%) and sequence divergence. Percentage of sequence divergence based on substitution and substitution plus indels is 44.15 and 57.19, respectively, for the ITS 1; 29.74 and 47.96% were recorded for the ITS 2. Although highly variable, conserved motifs within the ITS 1 and ITS 2 region of Nymphaea were identified and are found to be common throughout the order Nymphaeales. Sequence analysis of the ITS 1 and ITS 2 failed to detect any variation between two morphotypes of N. nouchali, namely N. nouchali JD 06 and N. nouchali JD 07, differing in flower color and found at the same geographical location. However, on comparison with another specimen of N. nouchali found at a different location, they showed considerable variation in nucleotide composition. Complemented by sequence data retrieved from GenBank, phylogenetic tree reconstruction of the genus Nymphaea based on neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference methods is presented and discussed.

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Acknowledgments

The authors acknowledge two anonymous reviewers for their valuable comments made on an earlier version of the manuscript. The authors are grateful to Dr. S. Goel, Delhi University, for generous help and suggestions. JD is thankful to Dr. R. Gogoi, Botanical Survey of India, Shillong, for necessary help in procuring N. nouchali JD 02. This work is part of a project sanctioned to PT and SK by the Department of Biotechnology, Ministry of Science and Technology, India (file no. BT/PR-7055/BCE/08/437/2006). JD is thankful to the University Grants Commission for awarding him the Rajiv Gandhi National Fellowship.

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  1. Plant Biotechnology Laboratory, Centre for Advanced Studies in Botany, North-Eastern Hill University, Shillong, 793 022, India

    Jeremy Dkhar, Suman Kumaria & Pramod Tandon

  2. Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793 022, India

    Satyawada Rama Rao

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  1. Jeremy Dkhar
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  2. Suman Kumaria
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  3. Satyawada Rama Rao
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Correspondence to Suman Kumaria.

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Dkhar, J., Kumaria, S., Rao, S.R. et al. Sequence characteristics and phylogenetic implications of the nrDNA internal transcribed spacers (ITS) in the genus Nymphaea with focus on some Indian representatives. Plant Syst Evol 298, 93–108 (2012). https://doi.org/10.1007/s00606-011-0526-z

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