Identification of the NAC Transcription Factor Family during Early Seed Development in Akebia trifoliata (Thunb.) Koidz

Abstract

This study aimed to gain an understanding of the possible function of NACs by examining their physicochemical properties, structure, chromosomal location, and expression. Being a family of plant-specific transcription factors, NAC (petunia no apical meristem and Arabidopsis thaliana ATAF1, ATAF2, and CUC2) is involved in plant growth and development. None of the NAC genes has been reported in Akebia trifoliata (Thunb.) Koidz (A. trifoliata). In this study, we identified 101 NAC proteins (AktNACs) in the A. trifoliata genome by bioinformatic analysis. One hundred one AktNACs were classified into the following twelve categories based on the phylogenetic analysis of NAC protein: NAC-a, NAC-b, NAC-c, NAC-d, NAC-e, NAC-f, NAC-g, NAC-h, NAC-i, NAC-j, NAC-k, and NAC-l. The accuracy of the clustering results was demonstrated based on the gene structure and conserved motif analysis of AktNACs. In addition, we identified 44 pairs of duplication genes, confirming the importance of purifying selection in the evolution of AktNACs. The morphology and microstructure of early A. trifoliata seed development showed that it mainly underwent rapid cell division, seed enlargement, embryo formation and endosperm development. We constructed AktNACs co-expression network and metabolite correlation network based on transcriptomic and metabolomic data of A. trifoliata seeds. The results of the co-expression network showed that 25 AtNAC genes were co-expressed with 233 transcription factors. Metabolite correlation analysis showed that 23 AktNACs were highly correlated with 28 upregulated metabolites. Additionally, 25 AktNACs and 235 transcription factors formed co-expression networks with 141 metabolites, based on correlation analysis involving AktNACs, transcription factors, and metabolites. Notably, AktNAC095 participates in the synthesis of 35 distinct metabolites. Eight of these metabolites, strongly correlated with AktNAC095, were upregulated during early seed development. These studies may provide insight into the evolution, possible function, and expression of AktNACs genes.

Genome-Wide Analysis of the Polygalacturonase Gene Family Sheds Light on the Characteristics, Evolutionary History, and Putative Function of Akebia trifoliata

“…Both the selection style and duplication type of members are the two most important factors when we investigate the evolutionary history of a given gene family. Here, we only found one homogenous gene pair (AktPG15 and AktPG17) with a Ka/Ks value (1.122) larger than 1 among a total of 467 homologous gene pairs, while all the others were less than 1 or even 0.5 (Supplementary Table S1), which suggested that AktPGs as well as AktNBSs [43], AktMADS-boxs [44], AktWRKYs [45], AktNACs [46], AktSODs [47], and AktDofs [48] experienced strong purifying selection in the evolutionary process.…”

Genome-Wide Identification and Characterization of the NAC Gene Family and Its Involvement in Cold Response in Dendrobium officinale

“…The NAC transcription factor family is a plant-specific transcription factor family, which plays key roles in stress response and tolerance by regulating the expression of stress-related genes in plants [1,40]. Previous studies have demonstrated that NAC genes also have a great impact on plant cold tolerance and some key cold-related regulation pathways have been revealed, such as the NAC-DREB and NAC-CBF-COR signaling pathways [41].…”

Genome-wide identification and molecular evolution of NAC gene family in Dendrobium nobile

“…The cis-acting element of the promoter region regulates the exact commencement of gene transcription and transcriptional efficiency by binding to transcription factors, it can determine the core area of transcriptional activation ( Wittkopp and Kalay, 2011 ; Ding et al., 2021 ; Liu et al., 2023 ; Rui et al., 2023 ). The NAC family has a substantial amount of cis-acting elements associated to light sensitivity, hormone response, biotic and abiotic stress response that are speculated to have a role in D. nobile growth and development, stress tolerance, and hormone signaling.…”

“…From the phylogenetic tree of NAC gene family in D. nobile, it can be seen that the D. nobile NAC gene family can be divided into 11 subfamilies and the family members are unevenly distributed in each subfamily. Combining the results of collinearity analysis and the phylogenetic tree of NAC gene family in D. nobile and Arabidopsis NAC gene family, it was discovered that there are eight pairings of genes with a high degree of similarity(DnoNAC27 The cis-acting element of the promoter region regulates the exact commencement of gene transcription and transcriptional efficiency by binding to transcription factors, it can determine the core area of transcriptional activation (Wittkopp and Kalay, 2011;Ding et al, 2021;Liu et al, 2023;Rui et al, 2023). The NAC family has a substantial amount of cis-acting elements associated to light sensitivity, hormone response, biotic and abiotic stress response that are speculated to have a role in D. nobile growth and development, stress tolerance, and hormone signaling.…”