Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China
Autor: | Mona B. Damaj, Lin Yihua, T. Erik Mirkov, San-Ji Gao, Rukai Chen, Yong-Bao Pan, Qin-Nan Wang |
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Rok vydání: | 2012 |
Předmět: |
China
food.ingredient Sequence analysis Molecular Sequence Data Genome Viral Luteoviridae Real-Time Polymerase Chain Reaction Polerovirus Open Reading Frames food Phylogenetics Sequence Homology Nucleic Acid Virology Genotype Genetics Cluster Analysis Molecular Biology Phylogeny Plant Diseases Genetic diversity biology Phylogenetic tree Reverse Transcriptase Polymerase Chain Reaction Sequence Analysis DNA General Medicine biology.organism_classification Saccharum Plant Leaves GenBank RNA Viral |
Zdroj: | Virus Genes. 45:340-349 |
ISSN: | 1572-994X 0920-8569 |
Popis: | Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family. |
Databáze: | OpenAIRE |
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