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

Abstract

NAC transcription factors are an important genes that regulate plant growth and development, and can regulate functions such as fruit ripening in plants. Based on genome data of Dendrobium nobile, the NAC gene family was identified and analyzed by bioinformatics methods. In this study, we identified 85 NAC genes in Dendrobium nobile genome, and systematically analyzed the NAC gene family. We found that they were distributed unevenly in the nineteen chromosomes. The amino acid length of D. nobile NAC gene family (DnoNACs) ranged from 80 to 1065, molecular weight ranged from 22.17 to 119.02 kD, and isoelectric point ranged from 4.61~9.26. Its promoter region contains multiple stress responsive elements, including light responsive, gibberellin-responsive, abscisic acid responsiveness, MeJA-responsiveness and drought-inducibility elements. Phylogenetic analysis indicates that the D. nobile NAC gene family is most closely related to Dendrobium catenatum and Dendrobium chrysotoxum. Analysis of SSR loci indicates that the fraction of mononucleotide repeats was the largest, as was the frequency of A/T. Non-coding RNA analysis showed that these 85 NAC genes contain 397 miRNAs. The collinearity analysis shows that 9 collinear locis were found on the chromosomes of D. nobile with Arabidopsis thaliana, and 75 collinear locis with D.chrysotoxum. QRT-PCR experiment under different salt concentration and temperature conditions verified the response mechanism of DnoNAC gene family under stress conditions. Most DnoNAC genes are sensitive to salt stress and temperature stress. The results of this study provide a reference for further understanding the function of NAC gene in D. nobile.

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development

“…There are 28 high-use codons (RSCU>1), 11 of which end in C, 10 of which end in U, 5 of which end in G, and 2 of which end in A. This result implies that the preferences for high-use codons terminate with C, However, low-use codons terminate with A, which is significantly distinct from the results of the NAC gene family in D.nobile (Fu and Liu, 2023). The heatmap clustering of codons RSCU of DnTCP genes revealed that members exhibit similar codon usage biases in same branch (Figure 6).…”

“…and PlantPAN 4.0 ( http://plantpan.itps.ncku.edu.tw/plantpan4/promoter_analysis.php ). Meanwhile, the essential codon metrics such as effective number of codons (ENc), codon adaptation index/bias index (CAI/CBI), and frequency of optimal codons (Fop) were determined using the CodonW1.4.2 program ( Wang et al., 2022 ; Fu and Liu, 2023 ). A heatmap clustering the relative synonymous codon usage (RSCU) of the TCP gene family in D. nobile was generated by using TBtools.…”

Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family

“…Through comprehensive analysis using relevant databases and software tools, a recent detailed study on Dendrobium nobile revealed the localization of DnoNACs as follows: 70 members in the nucleus, 6 in the chloroplast (DnoNAC11, DnoNAC12, DnoNAC23, DnoNAC30, DnoNAC69, and DnoNAC80), 3 in the cytoplasm (DnoNAC26, DnoNAC74, and DnoNAC78), 3 in the mitochondria (DnoNAC55, DnoNAC76, and DnoNAC83), and 3 in the peroxisome (DnoNAC16, DnoNAC17, and DnoNAC43) [78]. These locations align with those found for the Passiflora edulis NAC TF family [69].…”

“…Tumida [166], Liriodendrum [4], Hibiscus hamabo Sieb [167], and other species (see Introduction from [168]). Likewise, accumulated studies have shown that there are currently 117 NAC genes in Arabidopsis [169], 163 in poplar [170], 74 in Vitis vinifera [171], 85 in Liriodendrum [4], 151 in rice [54], 110 in potato [156], 152 in tobacco [172], 152 in soybean [154], 97 in Medicago truncatula [173], 104 in tomato [53], 204 in Chinese cabbage [174], 152 in maize [155], 85 in Dendrobium nobile [78], 150 in Helianthus annus [46], 105 in passion fruit (Passiflora edulis) [69], and 123 in Pinus tabuliformis [60]. Similarly, the genome-wide identification of NAC genes has been extended to numerous plant species (see Introduction and Discussion in [175]).…”

Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis

“…Their numbers are fewer only than those for bHLH, ERF and MYB. For example, 183 PbNAC genes were identified in white pear, 180 in apple, 167 NAC in cassava; 85 in Dendrobium nobile, 90 NAC in Dendrobium catenatum, 152 in Glycine max, 151 in Oryza sativa, and 226 such genes were identified in Triticum aestivum [46][47][48][49][50]. Recent studies have shown that the genes of the NAC family participate widely in various biological processes [51][52][53][54].…”