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Genome characterization of sugarcane yellow leaf virus

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Title Genome characterization of sugarcane yellow leaf virus
Not Available
 
Creator Viswanathan, R., C. Chinnaraja, R. Karuppaiah, K. Bhagyalakshmi, P. Malathi and B. Parameswari
 
Subject virus, genomic variation, SCYLV, ORF 1, ORF 5
 
Description Not Available
Detailed studies were carried out to characterize full genome of the virus and to establish genomic variation existing in Indian SCYLV population using six different sets of forward and reverse primers. We have characterized four SCYLV isolates infecting sugarcane cvs Co 86032, CoC 85061, CoV 92102 and B 38192 from India after complete genome sequencing. ORF 0 were compared between nt 200-770 (571 nt), ORF 1 between nt 200-1776 (1557 nt) and ORF 5 between nt 3579-4189 (610 nt) and their deduced amino acid sequences were also aligned. The new full length SCYLV nucleotide sequences (~ 5875 nt) were aligned along with those of five other available genotypes and all the sequences were trimmed to on equal length of 5616 nt on the basis of multiple sequence alignment to reduce errors with unequal length of sequences in identity matrix. Sequence analysis revealed that these isolates (SCYLV-IND) exhibited amino acid (aa) sequence differences of 29.2-31.8, 28.1-34.4 and 30.7-33.4% with REU, HAW-PER and BRA in partial ORF0 sequences, respectively. Similarly IND isolates have 21.4-23.7, 22.5-25.0 and 21.4-23.9% aa sequence differences with REU, HAW-PER and BRA, respectively in partial ORF 1. However, the difference was found to be least in ORF5 and it varied 3.0-6.0% and 3.0-6.9% with REU and HAW-PER/BRA sequences. A phylogram with other genotypes based on complete genomes showed that IND isolates shared 86.3- 86.6% with REU, 86.1-86.7% with BRA and 84.9-86.2% with the recently combined genotype of HAW-PER. The genotype reported from China, CHN1 shared a very close relationship with IND isolates with minimum differences of 4.3-5.3%, 4.8-5.8% and 2.5-3.0% in ORF0, 1 and 5 in aa sequences, respectively and 4.4-5.3% in complete nucleotide sequences.
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Date 2021-08-26T05:44:17Z
2021-08-26T05:44:17Z
2012-10-01
 
Type News Letter
 
Identifier Not Available
ICAR NEWS
http://krishi.icar.gov.in/jspui/handle/123456789/60605
 
Language English
 
Relation Not Available;
 
Publisher Directorate of Knowledge Management in Agriculture, Indian Council of Agricultural Research, New Delhi 110 012