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

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.

Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut

“…This expansion might arise from multiple gene duplication events, including whole-genome duplication in the Arachis lineage followed by multiple segmental and tandem duplication events [ 27 , 32 ]. These results were identical to those NAC from cultivated cotton Gossypium barbadense and two diploid cotton species, Gossypium rainondii and Gossypium arboreum [ 45 ]. Previous studies revealed that the involvement of NAC genes performed major functions in transcription regulation [ 45 ].…”

“…These results were identical to those NAC from cultivated cotton Gossypium barbadense and two diploid cotton species, Gossypium rainondii and Gossypium arboreum [45]. Previous studies revealed that the involvement of NAC genes performed major functions in transcription regulation [45]. Thus, we speculated that NACs might perform functions through regulating stress-resistant-related genes or proteins, while not performing functions like a "on-off" switch.…”

Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

“…In addition, the transcription levels of duplicated BdGATA gene pairs exhibited similar expression patterns, indicating that their role could be redundant. The functional redundancy of duplicated genes may be associated with the analogous CREs, gene models, and conserved motifs [ 38 ]. For instance, BdGATA7/19 duplicated pairs showed similar tertiary structures and expression patterns in response to M. oryzae inoculation, and both are predicted to interact with MBF proteins.…”

Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum

“…For Instance, 13 WRKY genes were identified on each of re-constructed G. arboreum A_A12 and G. raimondii D_D08 chromosomes with high collinearity. Recent study also reported highly conserved collinearity among TF-related genes of four Gossypium species [65]. In contrast, another study using previously assembled G. arboreum genome [27] identified different number of WRKY genes and their unobvious collinearity in G. arboreum and G. raimondii chromosomes 12, respectively [63].…”