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Evaluation of the diversity and phylogenetic implications of NAC transcription factor members of four reference species from the different embryophytic plant groups

Abstract

NAC transcription factors (TFs) are one of the largest and important TF family that are involved in the regulation of plant growth and development. They are characterized by a highly conserved N-terminal domain and a variable C-terminal domain. In the present study, the amino acid sequences of NAC TFs from four embryophytic plant species viz. Arabidopsis thaliana (Angiosperm), Picea abies (Gymnosperm), Selaginella moellendorffii (Pteridophyte) and Physcomitrella patens (Bryophyte) as reference of the different plant groups were collected from the Plant Transcription Factor Database (PTFD) and the phylogenetic relationships were evaluated. The phylogenetic tree revealed that the majority of the NAC members were interspersed in the major subgroups that indicated the expansion of the NAC members predates the speciation events. Thirty one (31), five (05), one (1) and ten (10) paralog pairs were determined respectively for Arabidopsis, Picea, Selaginella and Physcomitrella. The structure–function relationship of paralog pairs were inferred from the phylogenetic tree of combined set of paralogous gene pairs by studying the prevalence of flanking regions and motif analysis of the NAC proteins. The motif analysis revealed the presence of an N-terminal conserved domain, a characteristic of the majority of NAC family proteins. Conserved motifs in the C-terminal region were absent in the majority of the protein sequences except few members in Arabidopsis and Physcomitrella. Also the time of gene duplication of the paralog pairs were calculated that revealed the duplication events occurred between 4.48 and 45.94 MYA Arabidopsis, 167.57–532.86 MYA in Picea, and 29.12–53.53 MYA in Physcomitrella.

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Acknowledgements

The corresponding author is grateful to Dr. Vinay Singh, Information Officer, Centre for Bioinformatics, Banaras Hindu University, Varanasi, India for providing valuable inputs for the present study. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Correspondence to Swarnendu Roy.

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Chakraborty, R., Roy, S. Evaluation of the diversity and phylogenetic implications of NAC transcription factor members of four reference species from the different embryophytic plant groups. Physiol Mol Biol Plants 25, 347–359 (2019). https://doi.org/10.1007/s12298-018-0581-9

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Keywords

  • NAC transcription factors
  • Phylogenetic tree
  • Gene duplication
  • Motif analysis
  • Conserved domain