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Genome-Wide Identification and Analysis of GHMP Kinase Gene Superfamily in Bread Wheat (Triticum aestivum L.)

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Abstract

The GHMP (galactokinase, homoserine kinase, mevalonate kinase and phosphomevalonate kinase) kinase gene superfamily is a unique class of ATP-dependent enzymes. It plays a role in the metabolism of carbohydrate, biosynthesis of isoprenes, amino acids and nucleotide sugars. However, this important gene family has not been characterized in wheat (Triticum aestivum L.). In this study, total forty-seven putative GHMP kinase sequences were identified in wheat (Triticum aestivum L.) genome. Physicochemical properties, motif prediction, conserved domain and exon-intron configuration analyses revealed that these sequences were distributed in 10 subfamilies. Promoter analysis of GHMP kinase sequences showed that the cis-acting regulatory elements are involved in diverse functions such as light, stress, hormone and metabolism responsiveness, tissue-specific activation, circadian control, binding site and cell cycle regulation. Phylogenetic relationship with other monocot species has further strengthened the subfamily grouping pattern. The heat map presented by transcriptomic data analysis revealed that 25 and 12 genes showed significant differential expression against the abiotic and biotic stresses, respectively. The expression of selected genes was validated under abiotic stress conditions viz., heat, drought and their combination by qRT-PCR analysis. In conclusion, the present study provides novel information, thus enhances our understanding of the GHMP kinase gene family in wheat. The information obtained will be valuable in selecting potential candidate genes in wheat for developing cultivars with improved tolerance against biotic and abiotic stresses.

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Acknowledgements

We are grateful for the support and facilities provided by the National Agri-Food Biotechnology Institute (NABI), Mohali. The authors are thankful to DBT e-Library Consortium (DeLCON). N.T. and F. are thankful to the ICMR and DBT for a Senior Research Fellowship and Panjab University, Chandigarh, for Ph.D. registration.

Funding

This work was supported by NABI core grant. The funders had no role in the design of the study; in the collection, analyses and interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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Authors and Affiliations

  1. National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector-81, Knowledge City, S.A.S. Nagar, Mohali, 140306, India

    Neha Thakur,  Flowerika, Pankaj K. Singh, Karambir Kaur & Siddharth Tiwari

  2. Department of Biotechnology, Panjab University, Chandigarh, 160014, India

    Neha Thakur &  Flowerika

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  1. Neha Thakur
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  2. Flowerika
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  3. Pankaj K. Singh
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Contributions

S.T. conceived and designed the research. N.T. performed computational analysis. N.T. and P.K.S. performed transcriptomics data analysis. N.T. and F. contributed to the qRT-PCR experiments. N.T., F., P.K.S and K.K. analysed the data. N.T. and S.T wrote and revised the manuscript.

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Correspondence to Siddharth Tiwari.

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Key Message

The GHMP (galactokinase, homoserine kinase, mevalonate kinase and phosphomevalonate) kinase gene superfamily in wheat is unique as it consists of 10 different subfamilies, with each subfamily members being involved in different functions. The gene structural and functional features of the wheat-derived forty-seven GHMP kinases were predicted using various bioinformatics tools. Results from RNA-seq data analysis in this work will be helpful in selecting candidate genes for developing wheat varieties with enhanced tolerance against biotic and abiotic stresses.

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Thakur, N., Flowerika, Singh, P.K. et al. Genome-Wide Identification and Analysis of GHMP Kinase Gene Superfamily in Bread Wheat (Triticum aestivum L.). Plant Mol Biol Rep 39, 455–470 (2021). https://doi.org/10.1007/s11105-020-01259-2

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  • DOI: https://doi.org/10.1007/s11105-020-01259-2

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