Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Abstract

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

“…In this study, we identified a total of 114 genes encoding NAC protein in the J. mandshurica genome (Table S1). The number of NAC genes was significantly higher in J. mandshurica than that in Panax ginseng (89 PgNACs genes) [43], Phyllostachys heterocycla (94 PeNACs genes) [52], Xanthoceras sorbifolia (103 XsNACs genes) [26] and J. regia (102 JrNACs genes) [53] but was the same as in Betula pendula (114 BpNACs genes) [54] and Dimocarpus longan (114 DlNACs genes) [44], indicating high conservation of NAC gene family in J. mandshurica, which may be related to gene duplication during species formation and evolution. With regard to subcellular localization, all 114 JmNACs were predicted and located in the nucleus, which may be closely related to the expression regulation of target genes.…”

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

“…In this study, one member of the KNOX class (PeHB074) and two members of the BEL class (PeHB031, PeHB109) were positively co-expressed in the network, which was supported by the qRT-PCR results of them expressed in the shoots undergoing lignification. In addition, many studies have reported that TFs can regulate the lignin pathway by binding with the key structural genes involved in lignin synthesis [69]. For example, LTF1 acts as a regulator restraining lignin biosynthesis in poplar, which binds the promoter of a key lignin biosynthetic gene encoding 4-coumarate-CoA ligase (4CL) to regulate lignin biosynthesis [66].…”

AvNAC030, a NAC Domain Transcription Factor, Enhances Salt Stress Tolerance in Kiwifruit

“…We analyzed the sequence, length, distribution, and frequency of 20 conserved motifs of 120 VvNAC genes (Figure 2 and Table 2). Motif1, motif2, motif3, motif4, and motif5, which occur frequently, are mainly distributed at the N-terminal region of the NAC domain, indicating that these conservative motifs play an important role in the function of VvNAC [50]. Some less frequent motifs only appear in a specific subfamily.…”