Genome-wide analysis of evolution and expression profiles of NAC transcription factor gene family in Juglans regia L.

Hanif Khan,Feng Yan,Peng Zhao,Yujie Yan,Irfan Ullah,Xiaobang Peng,Ming Yue,Pengpeng Chen,Ruimin Xi,Xiang Luo

doi:10.1007/s13595-020-00983-9

Abstract

Key message NAC transcription factors may play important roles in the biological processes in Persian walnut. A total of 102 JrNAC s were identified in Persian walnut. The conserved domains, transcriptome profile, expression analysis, and interaction network suggest that JrNAC1-4 plays potential roles in Persian walnut flowering development. Context NACs are plant-specific transcription factors that participate in various plant developmental processes such as flowering, plant growth regulation, and development. We identified and analyzed the evolution and expression profiles of NAC genes in Juglans regia. Aims The main objectives were to identify the NAC transcription factors and verify the expression levels in different tissues and female flowers in developmental stages in Persian walnut. Methods We identified NAC transcription factors in J. regia based on the genome-wide analysis. We analyzed the phylogenetic relationships, conserved domain, chromosome location, gene structure, and gene collinearity of JrNACs. We also verified the JrNAC expression levels based on transcriptome analysis and qRT-PCR. Results We identified 102 NAC genes in J. regia and divided them into ten subfamilies. A total of 30 pairs of JrNAC genes were expanded by whole-genome duplications (WGDs) and one pair of genes (JrNAC2-10 and JrNAC9-8) as a tandem duplication in Persian walnut. Collinearity analysis results indicate that a large number of syntenic relationship events existed between J. regia and Populus trichocarpa. We found that JrNAC1-4 and JrNAC2-6 were expressed significantly higher in female flowers based on both transcriptome and qPCR analysis. We further identified that JrNAC2-9 and JrNAC9-6 were highly expressed at the end period of flowering stages. Conclusion A total of 102 JrNACs were identified in the Persian walnut genome. These genes were conserved in plants for collinearity analysis, which was performed within the genome and other genomes (P. trichocarpa, Olea europaea, and Quercus robur). A total of 24 NAC transcription factors were highly expressed in female and male flowers, and these transcription factors play a role in J. regia flowering.

Highlights

The NAC (NAM, ATAF1/2, and CUC) transcription factor (TF) family contains about ~ 150 amino acid residues and is the most important and largest TF family in plants that contains a conserved NAM domain at their N-terminus (Souer et al 1996; Tran et al 2010; Zhu et al 2012)
A total of 24 NAC transcription factors were highly expressed in female and male flowers, and these transcription factors play a role in J. regia flowering
In Persian walnut (J. regia), we identified a total of 102 NAC transcription factors

Summary

Introduction

The NAC (NAM, ATAF1/2, and CUC) transcription factor (TF) family contains about ~ 150 amino acid residues and is the most important and largest TF family in plants that contains a conserved NAM domain at their N-terminus (Souer et al 1996; Tran et al 2010; Zhu et al 2012). NAC transcription factors in many plants have been detected, such as in the model plant Arabidopsis, where a total of 105 NAC genes have been identified (Ooka et al 2003); in important annual crops Brassica pekinensis, Glycine max, Oryza sativa, Cajanus cajan, Setaria italica, Medicago truncatula, and Triticum turgidum (Nuruzzaman et al 2010; Le et al 2011; Puranik et al 2013; Liu et al 2014; Ling et al 2017; Saidi et al 2017); and perennial woody plants including Populus trichocarpa, Vitis vinifera, Prunus mume, Morus notabilis, and Malus domestica (Hu et al 2010; Su et al 2013; Satheesh et al 2014; Baranwal and Khurana 2016; Zhuo et al 2018)

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Discussion

Conclusion