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NAC transcription factor genes: genome-wide identification, phylogenetic, motif and cis-regulatory element analysis in pigeonpea (Cajanus cajan (L.) Millsp.)

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Abstract

The NAC (NAM, ATAF and CUC) proteins are plant-specific transcription factors implicated in development and stress responses. In the present study 88 pigeonpea NAC genes were identified from the recently published draft genome of pigeonpea by using homology based and de novo prediction programmes. These sequences were further subjected to phylogenetic, motif and promoter analyses. In motif analysis, highly conserved motifs were identified in the NAC domain and also in the C-terminal region of the NAC proteins. A phylogenetic reconstruction using pigeonpea, Arabidopsis and soybean NAC genes revealed 33 putative stress-responsive pigeonpea NAC genes. Several stress-responsive cis-elements were identified through in silico analysis of the promoters of these putative stress-responsive genes. This analysis is the first report of NAC gene family in pigeonpea and will be useful for the identification and selection of candidate genes associated with stress tolerance.

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Acknowledgments

We thank the Indian Council of Agricultural Research (ICAR), New Delhi, India for funding this work through the Network Project on Transgenics in Crops (NPTC). VS and PTKJ thank the Indian Agricultural Research Institute (IARI) for the Senior Research Fellowship. PC gratefully acknowledges the Senior Research Fellowship awarded by the Council of Scientific and Industrial Research (CSIR). The authors also gratefully acknowledge the critical comments of the reviewer.

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  1. National Research Centre on Plant Biotechnology, IARI, New Delhi, 110012, India

    Viswanathan Satheesh, P. Tej Kumar Jagannadham, Parameswaran Chidambaranathan, P. K. Jain & R. Srinivasan

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  1. Viswanathan Satheesh
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  2. P. Tej Kumar Jagannadham
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  3. Parameswaran Chidambaranathan
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Correspondence to R. Srinivasan.

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Viswanathan Satheesh, P Tej Kumar Jagannadham and Parameswaran Chidambaranathan have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table 1: Motif sequence and motif width of pigeonpea NAC genes identified through MEME. (XLS 2 kb)

Supplementary Fig. 1: Venn diagram showing the NAC proteins predicted by all three programmes. (JPG 634 kb)

11033_2014_3669_MOESM3_ESM.jpg

Supplementary Fig. 2 Phylogenetic reconstruction of Arabidopsis, soybean and pigeonpea NAC transcription factors using the Neighbor-joining method in MEGA5. (JPG 1,415 kb)

11033_2014_3669_MOESM4_ESM.jpg

Supplementary Fig. 3 Pigeonpea NAC genes containing transmembrane domain in the C-terminal region indicated as TM, NAC represents NAC domain. The TM is identified utilizing (http://aramemnon.botanik.uni-koeln.de) analysis tool. (JPG 719 kb)

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Satheesh, V., Jagannadham, P.T.K., Chidambaranathan, P. et al. NAC transcription factor genes: genome-wide identification, phylogenetic, motif and cis-regulatory element analysis in pigeonpea (Cajanus cajan (L.) Millsp.). Mol Biol Rep 41, 7763–7773 (2014). https://doi.org/10.1007/s11033-014-3669-5

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