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Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula, Sorghum bicolor, Vitis vinifera and Oryza sativa Using Comparative Genomics Approach

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Abstract

The polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment of Medicago truncatula, Vitis vinifera Sorghum bicolor, and Oryza sativa L. ssp. japonica genomes revealed 53, 49, 38 and 35 PG-like (PGL) genes, respectively. The predominance of glyco_hydro_28 domain, hydrophilic nature and genes with multiple introns were uniformly observed. The subcellular localization showed the presence of signal sequences targeting the secretory pathways. The phylogenetic tree constructed marked uniformity with three distinct clusters for each plant irrespective of the variability in the genome sizes. The site-specific selection pressure analysis based on K a/K s values showed predominance of purifying selection pressures among different groups identified in these plants. The functional divergence analysis revealed significant site-specific selective constraints. Results of site-specific selective pressure analysis throw light on the functional diversity of PGs in various plant processes and hence its constitutive nature. These findings are further strengthened by functional divergence analysis which reveals functionally diverse groups in all the four species representing monocots and dicots. The outcome of the present work could be utilized for deciphering the novel functions of PGs in plants.

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Acknowledgements

The financial support by Department of Science and Technology, Government of India, New Delhi, in the form of SERB Young Scientist Fellowship (SB/FT/LS-430/2012) to S. Yadav is thankfully acknowledged. GA would like to acknowledge Jawaharlal Nehru Memorial Fund for providing Jawaharlal Nehru Memorial Scholarship for doctoral studies. The authors acknowledge the infrastructural support from the Head, Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur.

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Authors and Affiliations

  1. Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh, 273 009, India

    Gautam Anand, Sangeeta Yadav, Aiman Tanveer, Jeya Nasim, Nitish K. Singh, Amit K. Dubey & Dinesh Yadav

  2. Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, India

    Nitish K. Singh

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  1. Gautam Anand
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  2. Sangeeta Yadav
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Correspondence to Dinesh Yadav.

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Anand, G., Yadav, S., Tanveer, A. et al. Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula, Sorghum bicolor, Vitis vinifera and Oryza sativa Using Comparative Genomics Approach. Interdiscip Sci Comput Life Sci 10, 704–721 (2018). https://doi.org/10.1007/s12539-017-0230-y

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