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Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China

Gao, San-Ji, Lin, Yi-Hua, Pan, Yong-Bao, Damaj, Mona B., Wang, Qin-Nan, Mirkov, T. Erik, Chen, Ru-Kai
Virus genes 2012 v.45 no.2 pp. 340
Saccharum, Sugarcane yellow leaf virus, clones, databases, genetic variation, genotype, hybrids, leaves, phylogeny, reverse transcriptase polymerase chain reaction, sugarcane, transcription (genetics), viruses, China
Sugarcane yellow leaf virus (SCYLV), the causal agent of sugarcane yellow leaf disease (YLD), was first reported in China in 2006. In order to determine the distribution existence of SCYLV in major sugarcane-growing provinces in China, leaf samples were collected from 22 sugarcane clones (Saccharum spp. hybrids) showing YLD symptoms and subjected to SCYLV diagnosis by reverse transcriptase PCR (RT-PCR), real-time RT-PCR, and serological methods. The complete genomic sequence of a Chinese SCYLV isolate CHN-FJ1 (5,879 nt) and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned and sequenced. The complete genomic sequence of CHN-FJ1 shared a high similarity value (98.8%-99.1%) with the isolates of BRA genotype and low similarity (86.1%-86.9%) with the two isolates of CHN1 genotype. Based on either the full or partial genomic sequences, the genetic diversity of these 14 Chinese SCYLV isolates was assessed along with 33 reported SCYLV isolates from the GenBank database representing worldwide origins. Phylogenetic analysis demonstrated that all the 14 Chinese isolates were clustered together in the BRA genotype group with seven other reported isolates. In addition, five reported Chinese SCYLV isolates were grouped in either genotype PER or genotype CHN1. Therefore, we speculated that at least three SCYLV genotypes (BRA, CHN1, and PER) were associated with YLD in China. Interestingly, a 49-nt deletion was found in the genomic sequence of CHN-GD3 isolate, locating in the middle of the ORF1 adjacent to the overlap between ORFs 1 and 2. This location was previously reported as one of the recombination breakpoints in the Luteoviridae family.