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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

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Title 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
 
Creator Mamathashree MN
Suresh KP
Patil SS
Indrabalan UB
Beelagi MS
Sushma P
Krishnamoorthy P
Siju SJ
Srinivasa C
Shiva PK
Raghu RA
Ashwini P
Shashanka KP
Shivamallu C
 
Subject Tomato yellow leaf curl virus (TYLCV)
Tomato
C1/AC1 protein gene
Asian countries
Codon usage bias
Evolutionary characters
Phylogeography analysis
Positive selection
tMRCA
 
Description Not Available
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 publicly 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.
Not Available
 
Date 2022-12-20T05:03:29Z
2022-12-20T05:03:29Z
2022-12-16
 
Type Research Paper
 
Identifier Mamathashree, M.N., Suresh, K.P., Patil, S.S., Indrabalan, U.B., Beelagi, M.S., Sushma, P., Krishnamoorthy, P., Siju, S.J., Srinivasa, C., Shiva, P.K., Raghu, R.A., Ashwini, P., Shashanka, K.P and Shivamallu, C. (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, 11(1):106-124.
2278-4292
http://krishi.icar.gov.in/jspui/handle/123456789/75224
 
Language English
 
Relation Not Available;
 
Publisher JSS University, Mysore