Genomic sequencing and analysis of Chilli ringspot virus, a novel potyvirus

• Published in: Virus genes Vol. 43; no. 3; pp. 439 - 444
• Main Authors: Gong, Dian, Wang, Jian-Hua, Lin, Zhan-Song, Zhang, Shao-Yan, Zhang, Yu-Liang, Yu, Nai-Tong, Xiong, Zhongguo, Liu, Zhi-Xin
• Format: Journal Article
• Language: English
• Published: New York Springer-Verlag 01.12.2011; Springer US; Springer Nature B.V
• Subjects: Amino acids; Base Sequence; Biomedical and Life Sciences; Biomedicine; Capsicum - virology; complementary DNA; genome; Genome, Viral; Genomic analysis; genomics; Medical Microbiology; Molecular Sequence Data; Nucleotides; open reading frames; Phylogeny; Plant Diseases - virology; Plant Sciences; Plant viruses; Potyvirus - classification; Potyvirus - genetics; Potyvirus - isolation & purification; reverse transcriptase polymerase chain reaction; Reverse transcription; sequence analysis; Tobacco vein banding mosaic virus; Virology; viruses; China; Potyvirus; Phylogeny; Genome; ChiRSV; Motif
• ISSN: 0920-8569; 1572-994X
• DOI: 10.1007/s11262-011-0652-2

Chilli ringspot virus (ChiRSV), a novel potyvirus, was recently found in Hainan, China with high prevalence. The genomic sequence of the ChiRSV-HN/14 isolate was determined by sequencing overlapping cDNA segments generated by reverse transcription polymerase chain reaction with degenerate and/or specific primers. ChiRSV genome (GenBank Acc. no. JN008909) comprised of 9,571 nucleotides (nt) excluding the 3′-terminal poly (A) tail and contained a large open reading frame of 9,240 nt encoding a large polyprotein of 3,079 amino acids with predicted Mr of 349.1 kDa. A small, overlapping PIPO coding region was also found to span from nt 2,913 to 3,095, with a capacity to encode a peptide of 60 amino acids. ChiRSV shares sequence identities of only 48.5–65.4 and 42.9–68.7% with closely related potyviruses at the nucleotide and the amino acid levels, respectively. Phylogenetic analysis of the genomic sequences provided further evidence that ChiRSV is a distinct species of the Potyvirus genus. ChiRSV-HN/14 is most closely related to Tobacco vein banding mosaic virus and two other pepper-infecting potyviruses.