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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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.
KeywordsPolygalacturonases-like (PGL) genes Pectinases Phylogenetic tree Functional divergence Subcellular localization Genomics
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.
- 14.Chaudhri A, Suneetha V (2012) Microbially derived Pectinases: a review. IOSR J Pharm Biol Sci 2(2):1–5Google Scholar
- 15.Dubey AK, Yadav S, Kumar M, Anand G, Yadav D (2016) Molecular biology of microbial pectate lyases: a review, British. Biotechnol J 13(1):1–26Google Scholar
- 18.Dubey AK, Yadav S, Rajput R, Anand G, Yadav D (2012) In silico characterization of bacterial, fungal and plant polygalacturonase protein sequences. Online J Bioinform 13:246–259Google Scholar
- 19.Lara-Marquez A, Zavala-Paramo MG, Lopez-Romero E, Calderon-Cortes N, Lopez-Gomez R, Conejo-Saucedo U, Cano-Camacho H (2011) Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms. BMC Microbiol. https://doi.org/10.1186/1471-2180-11-260 CrossRefPubMedPubMedCentralGoogle Scholar
- 39.Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Apple RD, Bairoch A (2002) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The Proteomics Protocols Handbook. Humana Press, New york, pp 571–607Google Scholar
- 48.Sander L, Child R, Ulvskov P, Albrechtsen M, Borkhardt B (2001) Analysis of a dehiscence endo-polygalacturonase in oilseed rape (Brassica napus) and Arabidopsis thaliana: evidence for roles in cell separation in dehiscence & abscission zones, and in stylar tissues during pollen tube growth. Plant Mol Biol 46(4):469–479CrossRefGoogle Scholar