Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

Abstract

The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001–PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein–protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.

Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic

“…In this study, most of the AsNAC proteins had all of the five subdomains, whereas some domain regions were incomplete in the minority proteins. Similar results were also observed in some previous studies ( He et al, 2022 ; Yang et al, 2022 ), indicating that some NAC proteins possessed preternatural structures and unique functions. It is reported that subdomains A, C, and D are more conserved than B and E ( Ooka et al, 2003 ; Wang et al, 2016 ).…”

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

“…Interestingly, our findings were inconsistent with the analysis of Passiflora edulis NAC protein interactions. This we related to the differences in the development processes of LchibZIP proteins and PeNAC proteins long-term domestication ( Yang et al., 2022 ).…”

Identification and Expression Analysis of the Solanum tuberosum StATG8 Family Associated with the WRKY Transcription Factor

“…It can be expected that StATG8 genes can be regulated using the WRKY transcription factor [ 42 ]. From the previous reports, autophagy plays an important role in development [ 43 , 44 ]; the regulatory elements CCGTCC motif, RY-element, MSA-like, and GCN4-motif related to development were present in StATG8 promoters ( Figure 2 and Table 1 ) [ 45 ]. Thus, the diverse StATG8 genes are deeply associated with multiple stress responses and developments.…”