Research Article A new Informatics Framework for Evaluating the Codon Usage Metrics, Evolutionary Models and Phylogeographic reconstruction of Tomato yellow leaf curl virus (TYLCV) in different regions of Asian countries

Authors

Mamathashree Mn, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Kuralyanapalya Putta Honnappa Suresh, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Sharanagouda S Patil, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Uma Bharathi Indrabalan, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Mallikarjun S Beelagi, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Sushma Pradeep, Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Karnataka, 570015, Mysore, India
Krishnamoorthy Paramanandham, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Siju Susan Jacob, ICARNational Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru560064, Yelahanka, India
Chandrashekar Srinivasa, Department of Biotechnology, Davangere University, Davangere -577002, Karnataka, Shivagangotri, India
Shiva Prasad Kollur, School of Agriculture, Geography, Environment, Ocean and Natural Sciences, The University of the South Pacific, Laucala Campus, Suva, Fiji
Raghu Ram Achar, Department of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Karnataka, Mysore, India
Ashwini Prasad, Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Karnataka, Mysore, India
Shashanka K Prasad, Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Karnataka, 570015, Mysore, India
Chandan Shivamallu, Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Karnataka, 570015, Mysore, IndiaFollow

Abstract

Tomato yellow leaf curl virus (TYLCV) is a major devastating viral disease, majorly affecting the tomato production globally. The disease is majorly transmitted by the Whitefly. The Begomovirus (TYLCV) having a six major protein coding genes, among them the C1/AC1 is evidently associated with viral replication. Owing to immense role of C1/AC1 gene, the present study is an initial effort to elucidate the factors shaping the codon usage bias and evolutionary pattern of TYLCV-C1/AC1 gene in five major Asian countries. Based on publically available nucleotide sequence data the Codon usage pattern, Evolutionary and Phylogeographic reconstruction was carried out. The study revealed the presence of significant variation between the codon bias indices in all the selected regions. Implying that the codon usage pattern indices (eNC, CAI, RCDI, GRAVY, Aromo) are seriously affected by selection and mutational pressure, taking a supremacy in shaping the codon usage bias of viral gene. Further, the tMRCA age was 1853, 1939, 1855, 1944, 1828 for China, India, Iran, Oman and South Korea, respectively for TYLCV-C1/AC1 gene. The integrated analysis of Codon usage bias, Evolutionary rate and Phylogeography analysis in viruses signifies the positive role of selection and mutational pressure among the selected regions for TYLCV (C1/AC1) gene.

Recommended Citation

Mn, Mamathashree; Suresh, Kuralyanapalya Putta Honnappa; Patil, Sharanagouda S; Indrabalan, Uma Bharathi; Beelagi, Mallikarjun S; Pradeep, Sushma; Paramanandham, Krishnamoorthy; Jacob, Siju Susan; Srinivasa, Chandrashekar; Kollur, Shiva Prasad; Achar, Raghu Ram; Prasad, Ashwini; Prasad, Shashanka K; and Shivamallu, Chandan (2022) "Research Article A new Informatics Framework for Evaluating the Codon Usage Metrics, Evolutionary Models and Phylogeographic reconstruction of Tomato yellow leaf curl virus (TYLCV) in different regions of Asian countries," International Journal of Health and Allied Sciences: Vol. 11: Iss. 1, Article 15.
DOI: 10.55691/2278-344X.1016
Available at: https://rescon.jssuni.edu.in/ijhas/vol11/iss1/15