Identification and Analysis of the NAC Transcription Factors Gene Family in Cucurbita moschata Duch.

doi:10.13560/j.cnki.biotech.bull.1985.2025-1069

Abstract

Abstract:

Objective We investigated the structural characteristics and expression patterns of CmoNAC genes in Cucurbita moschata,which provides insights into the biological functions of CmoNAC genes and facilitates the breeding of stress-resistant rootstock and hull-less seeded C. moschata. Method Based on the whole genome information of C. moschata, CmoNAC gene family members were identified using bioinformatic approaches. Systematic analyses were conducted on the physicochemical properties, subcellular localization, chromosomal localization, gene structure, and conserved motifs of its members. By integrating transcriptome data and quantitative real-time PCR (RT-qPCR), the tissue-specific expression patterns of CmoNAC genes, as well as their responses to stress and their roles in seed coat development, were investigated. Result The CmoNAC gene family comprises 133 members, all of which encode proteins predominantly localized in the nucleus and contain a typical NAM domain. These members are unevenly distributed across 20 chromosomes, with chromosome 4 harboring the highest number. Phylogenetic analysis classified them into 15 subfamilies, among which the NAM subfamily is the largest. Conserved Motif and gene structure analyses revealed that members within the same subfamily share similar motif compositions and exon-intron structures. Motifs 2/3/4 were widely present across most members, while some Motifs presented subfamily-specific distribution. Cis-acting element analysis indicated that the promoter regions of CmoNACs contain various regulatory elements related to light responsiveness, hormone signaling, stress response, and developmental processes. Tissue-specific expression analysis revealed that CmoNAC family members had the highest expressions in the roots. Among the CmoNAC genes in C. moschata, 100 ones were significantly upregulated under salt stress. Furthermore, 64 members showed differential expression between hull and hull-less seeded C. moschata. RT-qPCR showed the expression patterns of CmoNAC genes under salt stress and during seed coat development were consistent with the transcriptome data. Conclusion A total of 133 CmoNAC genes are identified in the C. moschata genome, which could be classified into 15 subfamilies. The gene structure and conserved motifs are highly conserved within each subfamily. CmoNAC108, CmoNAC102, and CmoNAC013 are respectively closely associated with root, stem development and stress responses while CmoNAC026, CmoNAC062 and CmoNAC121 are specifically upregulated in hull-less seeds, suggesting their potential roles in the formation of the seed coat.

Key words: Cucurbita moschata, NAC gene family, phylogenetic analysis, conserved motif, cis-acting element, salt stress response, seed coat development, tissue-specific expression

MENG Hong-yu, LIU Ya-nan, WU Jun-xin, SHEN Qiong. Identification and Analysis of the NAC Transcription Factors Gene Family in Cucurbita moschata Duch.[J]. Biotechnology Bulletin, 2026, 42(6): 237-249.

Figures/Tables 9

Fig. 1 Chromosomal distribution of NAC gene family in C. moschata

Fig. 2 Phylogenetic tree of NAC protein in C. moschata (133) and A. thaliana (105)

Fig. 3 Structure distribution patterns and domains prediction of the NAC gene family in C. moschataA: Protein conserved motif analysis. B: Gene structure analysis. C: Gene conserved domain analysis

Fig. 4 Prediction of cis-acting elements of the NAC gene family in C. moschata

Fig. 5 Analysis of the protein interaction network of the NAC gene family in C. moschata

Fig. 6 Expression patterns in various tissues of the NAC gene family in C. moschata and its expression analysis in response to salt stressL, S, F, and R indicates leaves, stems, fruits and roots, respectively. 0: 0 mmol/L NaCl; 75: 75 mmol/L NaCl

Fig. 7 Expression analysis of NAC gene family in seed coat of hull and hull-less seeded C. moschata at different developmental stagesHS-A-15, HS-A-20, HS-A-30: The expressions of the gene in the seed coat of seeded pumpkin HS-A at 15, 20 and 30 DPA. HLS-B-15, HLS-B-20, HLS-B-30: The expressions of the gene in the seed coat of hull-less pumpkin HLS-B at 15, 20 and 30 DPA. The same below

Fig. 8 Relative expressions of 15 CmoNACs genes under salt stress of C. moschataDifferent lowercase letters indicate significant difference at P0.05 level. The same below

Fig. 9 Relative expressions of 15 CmoNACs during the development of C. moschata seeds

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