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Transcriptome-wide identification and characterization of the regulatory landscape of NAC genes in Drimia indica

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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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Correspondence to Manoj Kumar.

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The authors declare no competing interests.

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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

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