Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt.

Zhanji Liu,Yizhen Chen,Liguo Wang,Hao Li,Mingchuan Fu,Renzhong Liu

doi:10.7717/peerj.7995

Abstract

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

Highlights

The plant-specific NAC genes (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor; and CUC, cup-shaped cotyledon) form one of the largest families of transcription factors (Nuruzzaman, Sharoni & Kikuchi, 2013)
This study provides comprehensive information about sea-island cotton NAC genes, as well as a foundation for in-depth functional analysis of novel GbNAC candidate genes, which may be useful for the improvement of pathogen resistance in cotton
We found that GbNAC genes in the same group had a similar gene structure

Summary

Introduction

The plant-specific NAC genes (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor; and CUC, cup-shaped cotyledon) form one of the largest families of transcription factors (Nuruzzaman, Sharoni & Kikuchi, 2013). The NAC domain can be further divided into five subdomains (A–E) and functions as DNA binding, nuclear localization, and formation of homodimers or heterodimers, while the TR region is responsible for transcription regulation as either an activator or a repressor (Olsen et al, 2005). NAM, the first NAC gene, was discovered in Petunia and functions in determining positions of shoot apical meristems and primordia (Souer et al, 1996). A large number of NAC genes have been identified from diverse plant species (Nuruzzaman et al, 2010; Liu et al, 2019)

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Conclusion