Genome-wide identification of NAC transcription factor family and expression analysis of ATAF subfamily members under abiotic stress in eggplant

Wan, Faxiang; Gao, Jun; Wang, Guang-Long; Niu, Yuan; Wang, Lianzhen; Zhang, Xingguo; Wang, Yongqing; Pan, Yu

doi:10.1016/j.scienta.2021.110424

Cited by 12 publications

(5 citation statements)

References 57 publications

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“…It has been reported that within the same gene family, the distribution of genes on different chromosomes may be due to their involvement in multiple functions ( Ahmad et al, 2021 ). The 105 PeNAC genes identified in the passion fruit genome were almost similar to the number of NAC genes in apricot (102 NAC ) ( Xu et al, 2021 ), pepper (104 NAC ) ( Diao et al, 2018 ), and cacao (102 NAC ) ( Shen et al, 2019 ), while some species have a larger number of NAC genes including rice (151 NAC ) ( Ooka et al, 2003 ), poplar (163 NAC ) ( Hu et al, 2010 ), apple (180 NAC ) ( Su et al, 2013 ), and barley (167 NAC ) ( Murozuka et al, 2018 ), whereas some species have a smaller number of NAC genes including maize (87 NAC ) ( Wang G. et al, 2020 ), pitaya (64 NAC ) ( Hu et al, 2022 ), and eggplant (90 NAC ) ( Wan et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“… Asefpour Vakilian (2020) reported that the miRNA plays a significant role under plant stresses. In recent years, with the development of bioinformatics, molecular biology techniques and the crucial role of NAC genes, the gnome wide identification of NAC genes has already been reported in numerous plants including 117 NAC genes in Arabidopsis and 151 in rice ( Ooka et al, 2003 ), 87 genes in maize ( Wang G. et al, 2020 ), 145 genes in sorghum ( Sorghum bicolor ) ( Kadier et al, 2017 ), 132 genes in peanut ( Arachis hypogaea ) ( Li P. et al, 2021 ), 113 genes in Medicago sativa ( Min et al, 2020 ), 90 genes in eggplant ( Solanum melongena ) ( Wan et al, 2021 ), 102 genes in apricot ( Prunus sibirica ) ( Xu et al, 2021 ), and cacao ( Theobroma cacao ) ( Shen et al, 2019 ), 167 genes in barley ( Murozuka et al, 2018 ), 64 genes in pitaya ( Hylocereus ) ( Hu et al, 2022 ), 114 genes in walnut ( Juglans mandshurica ) ( Li X. et al, 2021 ), 114 genes in longan ( Dimocarpus longan ) ( Munir et al, 2020 ), 154 genes in tobacco ( Nicotiana tabacum ) ( Li et al, 2018 ), 91 genes in cucumber ( Cucumis sativus ) ( Liu et al, 2018 ), 180 genes in apple ( Malus domestica ) ( Su et al, 2013 ), 147 genes in foxtail millet ( Setaria italica ) ( Puranik et al, 2013 ), 55 genes in jujuba ( Ziziphus jujuba ) ( Li M. et al, 2021 ), 163 genes in poplar ( Populus Trichocarpa ) ( Hu et al, 2010 ), 152 genes in soyabean ( Glycine max ) ( Le et al, 2011 ), and 104 genes in pepper ( Capsicum annuum ) ( Diao et al, 2018 ), respectively. However, the NAC gene family has not been studied in passion fruit.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

Rizwan

Sun

et al. 2022

Front. Plant Sci.

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The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001–PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein–protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

Rizwan

Sun

et al. 2022

Front. Plant Sci.

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“…Similarly, non-Gramineous peanut (Leguminosae) has 116 fragment replications compared to only 1 pair of tandem replication [ 28 ]. However, Solanum melongena (Solanaceae) has more tandem replication than fragment replication [ 29 ]. These findings suggest that angiosperms primarily use fragment replication.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of NAC Gene Family and Expression Analysis under Abiotic Stresses in Avena sativa

Ling

Chen

et al. 2023

Genes

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In this study, a total of 177 NAC members were identified in Avena sativa, located on 21 chromosomes. Phylogenetic analysis showed that AsNAC proteins could be divided into seven subfamilies (I–VII), and that proteins in the same subfamily have similar protein motifs. Gene structure analysis found that NAC introns ranged from 1 to 17. Cis-element analysis of the promoter indicated that the gene family may have stress-related elements and growth regulation elements. Through qRT-PCR experiments, we speculated that AsNACs genes can respond to abiotic stresses such as cold, freezing, salt, and saline alkali. This study provides a theoretical basis for further exploring the function of the NAC gene family in A. sativa.

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“…Among them, there are relatively more studies on ATAF subfamily genes. Wan et al [35] conducted RT-qPCR tests on SmNAC19, SmNAC31, and SmNAC75, three members of the ATAF subfamily of eggplant, and confirmed that they had significant responses to abiotic stresses such as low temperature, high temperature, drought, and hormones within 24 h. However, the peak value of the response to different stresses was different. Wang et al [36] and He et al [37] studied CsATAF1 in cucumber and GhATAF1 in cotton, respectively, and confirmed that ATAF family genes can improve plant tolerance to abiotic stresses such as drought and high salt.…”

Section: Motif and Pb Response Characteristics Of Sinac Of The Ataf A...mentioning

confidence: 96%

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

Yue

Huang

et al. 2023

IJMS

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The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were “sulfur metabolism” and “glutathione metabolism”, and the target pathways of NAP subfamily SiNACs were “ribosome” and “phenylpropanoid biosynthesis”. This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

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Genome-wide identification of NAC transcription factor family and expression analysis of ATAF subfamily members under abiotic stress in eggplant

Cited by 12 publications

References 57 publications

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

Genome-Wide Identification of NAC Gene Family and Expression Analysis under Abiotic Stresses in Avena sativa

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

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