Abstract
This study was aimed at understanding the role of the NAC transcription factor (TF) gene family in the development and stress responses of Drimia indica, a medicinal plant with immense therapeutic potential, to enhance its medicinal and agronomic traits. We identified and characterized 61 nonredundant putative NAC TF genes, and analyzed their physicochemical properties. The putative proteins encoded by these genes varied in their amino acid composition, molecular weight, and isoelectric point. The proteins were predicted to localize to different subcellular regions, mainly to the nucleus. The NAC genes were classified into 17 phylogenetic subgroups, which differed between D. indica and Arabidopsis thaliana. Gene structure analysis revealed a conserved CDS organization within each subfamily. The identified genes contained 10 conserved motifs, with “Motif 5” being the most prevalent. Promoter analysis revealed cis-elements responsive to light, abscisic acid, methyl jasmonate, and MYB transcription factors. Additionally, TF-binding site analysis revealed several protein families potentially regulating the expression of NAC genes. miRNA target analysis highlighted the potential role of miRNAs in the post-transcriptional regulation of NAC genes. Our findings offer valuable insights into the structural characteristics, regulatory mechanisms, and potential functions of the NAC TF gene family in D. indica, and advance our understanding of plant stress responses. These findings should provide future research avenues for modulating stress tolerance and secondary metabolite production.
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Abbreviations
- NAC:
-
NAM, ATAF1/2, and CUC2
- CDS:
-
Coding sequence
- UTR:
-
Untranslated region
- LR:
-
Light-responsive
- ABRE:
-
Abscisic acid responsive element
- MeJA:
-
Methyl jasmonate
- MYB-LR:
-
MYB transcription factor-responsive
- TFBS:
-
Transcription factor binding site
- miRNA:
-
MicroRNA
- HMM:
-
Hidden Markov model
- RNA-seq:
-
RNA-sequencing
- pI:
-
Isoelectric point
- NCBI:
-
National Center for Biotechnology Information
- BLAST:
-
Basic local alignment search tool
- ML:
-
Maximum likelihood
- ANAC:
-
Arabidopsis NAC
- GATA:
-
GATA transcription factor family
- Dof:
-
DNA binding with one finger
- HD-ZIP:
-
Homeodomain-leucine zipper
- TCP:
-
Teosinte branched/cycloidea/PCF
- MIKC_MADS:
-
MIKC-type MADS-box
- bHLH:
-
Basic helix-loop-helix
- ERF:
-
Ethylene-responsive element-binding factor
- RNA:
-
Ribonucleic acid
- qPCR:
-
Quantitative polymerase chain reaction
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Acknowledgements
We acknowledge the University Grants Commission (UGC) of India for generously funding this research through a fellowship (No. F. 82 − 44/2020 (SA-III)). We also acknowledge the assistance and resources provided by the Central University of Jharkhand, Ranchi.
Funding
This research was funded by the University Grants Commission (UGC), India, under fellowship No. F. 82 − 44/2020 (SA-III).
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Vivek Shit and Manoj Kumar conceptualized this study and designed the experiments. Vivek Shit performed the experiments, collected data, and contributed to data analysis and interpretation. Mahesh Kumar Dhakar provided critical feedback and revised the manuscript. All authors reviewed and approved the final version of the manuscript.
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Shit, V., Dhakar, M.K. & Kumar, M. Transcriptome-wide identification and characterization of the regulatory landscape of NAC genes in Drimia indica. Genet Resour Crop Evol (2023). https://doi.org/10.1007/s10722-023-01814-2
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DOI: https://doi.org/10.1007/s10722-023-01814-2