Genome-Wide Characterization and Comprehensive Analysis of NAC Transcription Factor Family in Nelumbo nucifera

Song, Heyun; Liu, Yanling; Gao, Dong; Zhang, Minghua; Wang, Yuxin; Xin, Jia; Su, Yanyan; Yang, Mei

doi:10.3389/fgene.2022.901838

Cited by 9 publications

(8 citation statements)

References 74 publications

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“…The number of introns in the KoNAC genes varied from 1 to 7, similar to numbers reported in many plant species ( Liu et al., 2019 ; Shan et al., 2020 ; Song et al., 2022 ). In general, the deletion or insertion of introns can result in a loss of gene function.…”

Section: Discussionsupporting

confidence: 80%

“…Many studies have been conducted to clarify the function of NAC TFs in reactions to various environmental stresses, such as salinity, drought, heat and flooding ( Fang et al., 2015 ; Yuan et al., 2020 ; Song et al., 2022 ). In the present study, the average expression level of the KoNACs was highest in roots, and a large number of KoNAC genes showed high levels of expression, such as KoNAC25 , KoNAC33 , KoNAC36 , KoNAC64 , KoNAC67 , KoNAC70 , KoNAC71 , and KoNAC75 ( Figure 8B ).…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

You

Yang

et al. 2022

Front. Plant Sci.

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BackgroundKandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.MethodsThe KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.ResultsA total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.ConclusionsSeventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

You

Yang

et al. 2022

Front. Plant Sci.

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“…However, functional research of lotus NAC genes has rarely been reported. Eighty-two NAC genes were obtained using the website PlantTFDB, and we studied their potential functions in lotus seeds and response to complete submergence [ 61 ]. Compared to NAC genes of other plants, the number NAC genes in lotus root still needs to be found.…”

Section: Discussionmentioning

confidence: 99%

Identification of the NAC Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

Zhao

Jiang

Zhang

et al. 2022

IJMS

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Nelumbo nucifera Gaertn. is an important perennial aquatic herb that has high ornamental, edible, medicinal, and economic value, being widely distributed and used in China. The NAC superfamily (NAM, ATAF1/2, CUC2) plays critical roles in plant growth, development, and response to abiotic and biotic stresses. Though there have been a few reports about NAC genes in lotus, systematic analysis is still relatively lacking. The present study aimed to characterize all the NAC genes in the lotus and obtain better insights on the NnNACs in response to salt stress by depending on ABA signaling. Here, 97 NAC genes were identified by searching the whole lotus genome based on the raw HMM models of the conserved NAM domain and NAC domain. They were characterized by bioinformatics analysis and divided into 18 subgroups based on the phylogenetic tree. Cis-element analysis demonstrated that NAC genes are responsive to biotic and abiotic stresses, light, low temperature, and plant hormones. Meanwhile, NAC genes had tissue expression specificity. qRT-PCR analysis indicated that NAC genes could be upregulated or downregulated by NaCl treatment, ABA, and fluoridone. In addition, NAC016, NAC025, and NAC070, whose encoding genes were significantly induced by NaCl and ABA, were located in the nucleus. Further analysis showed the three NAC proteins had transcriptional activation capabilities. The co-expression network analysis reflected that NAC proteins may form complexes with other proteins to play a role together. Our study provides a theoretical basis for further research to be conducted on the regulatory mechanisms of salinity resistance in the lotus.

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“…At present, more data on NAC transcription factors of plants have been collected from studies based on plant genomics [ 24 , 25 ] and bioinformatics [ 26 ]. Moreover, NAC transcription factors have promising applications in plant molecular breeding.…”

Section: Introductionmentioning

confidence: 99%

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

Liu

Chen

et al. 2023

Plants

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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.

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Genome-Wide Characterization and Comprehensive Analysis of NAC Transcription Factor Family in Nelumbo nucifera

Cited by 9 publications

References 74 publications

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

Identification of the NAC Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

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

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