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Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco (Nicotiana tabacum)

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Abstract

The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I–XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco.

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Acknowledgements

We thank Dr. Sanchita and Dr. Yogita Deshmukh for correcting the manuscript. The authors acknowledge HPC facility, CSIR-4PI, Bangaluru. This work was supported by a research grant (OLP 0104) from Council of Scientific and Industrial Research (CSIR), India. NB acknowledges UGC SRF fellowship. The manuscript number is provided by the institute is CSIR-NBRI_MS/2020/12/04.

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  1. Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India

    Nasreen Bano, Preeti Patel, Debasis Chakrabarty & Sumit Kumar Bag

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Nasreen Bano, Debasis Chakrabarty & Sumit Kumar Bag

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  1. Nasreen Bano
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NB carried out the bioinformatics analysis, design, and drafted the manuscript. PP performed quantitative expression analysis. DC and SKB participated in supervision of the study. All the authors read and approved the final manuscript.

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Correspondence to Sumit Kumar Bag.

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Bano, N., Patel, P., Chakrabarty, D. et al. Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco (Nicotiana tabacum). Physiol Mol Biol Plants 27, 1747–1764 (2021). https://doi.org/10.1007/s12298-021-01042-x

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  • DOI: https://doi.org/10.1007/s12298-021-01042-x

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