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Analysis of phylogenetic and functional diverge in plant nine-cis epoxycarotenoid dioxygenase gene family

Abstract

During different environmental stress conditions, plant growth is regulated by the hormone abscisic acid (an apocarotenoid). In the biosynthesis of abscisic acid, the oxidative cleavage of cis-epoxycarotenoid catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED) is the crucial step. The NCED genes were isolated in numerous plant species and those genes were phylogenetically investigated to understand the evolution of NCED genes in various plant lineages comprising lycophyte, gymnosperm, dicot and monocot. A total of 93 genes were obtained from 48 plant species to statistically estimate their sequence conservation and functional divergence. Selaginella moellendorffii appeared to be evolutionarily distinct from those of the angiosperms, insisting the substantial influence of natural selection pressure on NCED genes. Further, using exon–intron structure analysis, the gene structures of NCED were found to be conserved across some species. In addition, the substitution rate ratio of non-synonymous (Ka) versus synonymous (Ks) mutations using the Bayesian inference approach, depicted the critical amino acid residues for functional divergence. A significant functional divergence was found between some subgroups through the co-efficient of type-I functional divergence. Our results suggest that the evolution of NCED genes occurred by duplication, diversification and exon intron loss events. The site-specific profile and functional diverge analysis revealed NCED genes might facilitate the tissue-specific functional divergence in NCED sub-families, that could combat different environmental stress conditions aiding plant survival.

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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. The authors thank the anonymous reviewer for their insightful review of an earlier version of this manuscript.

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Correspondence to Ramamoorthy Siva.

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10265_2015_726_MOESM1_ESM.doc

Supplementary material 1 (DOC 38 kb) Fig. S1 Phylogenetic tree were constructed for 93 Nine-cis-epoxycarotenoid dioxygenase genes. This NJ tree was inferred from the amino acid sequences alignment using the PHYLIP v.3.69 and MEGA v5.05. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown above the branches

10265_2015_726_MOESM2_ESM.doc

Supplementary material 2 (DOC 670 kb) Fig. S2 Sequence alignment of NCED genes to identify the conserved region which is indicated in asterisk symbol

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Priya, R., Siva, R. Analysis of phylogenetic and functional diverge in plant nine-cis epoxycarotenoid dioxygenase gene family. J Plant Res 128, 519–534 (2015). https://doi.org/10.1007/s10265-015-0726-7

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Keywords

  • Apocarotenoids
  • Bayesian analyses
  • Evolution
  • Functional divergence
  • Phylogenetic relationship