Molecular Variability and Distribution of Sugarcane Mosaic Virus in Shanxi, China

Abstract

Background: Sugarcane mosaic virus (SCMV) is responsible for large-scale economic losses in the global production of sugarcane, maize, sorghum, and some other graminaceous species. To understand the evolutionary mechanism of SCMV populations, this virus was studied in Shanxi, China. A total of 86 maize leaf samples (41 samples in 2012 and 45 samples in 2013) were collected from 4 regions of Shanxi.

Results: Double-antibody sandwich (DAS)-ELISA and RT-PCR showed 59 samples (30 samples in 2012 and 29 samples in 2013) to be positive for SCMV, from which 10 new isolates of SCMV were isolated and sequenced. The complete genomes of these isolates are 9610 nt long, including the 5' and 3' non-coding regions, and encode a 3063-amino acid polyprotein. Phylogenetic analyses revealed that 24 SCMV isolates could be divided on the basis of the whole genome into 2 divergent evolutionary groups, which were associated with the host species. Among the populations, 15 potential recombination events were identified. The selection pressure on the genes of these SCMV isolates was also calculated. The results confirmed that all the genes were under negative selection.

Conclusions: Negative selection and recombination appear to be important evolutionary factors shaping the genetic structure of these SCMV isolates. SCMV is distributed widely in China and exists as numerous strains with distinct genetic diversity. Our findings will provide a foundation for evaluating the epidemiological characteristics of SCMV in China and will be useful in designing long-term, sustainable management strategies for SCMV.

Fig 1. Sugarcane mosaic virus genome structure and potential recombination events.

The RNA genome of SCMV, including the untranslated region (UTR) at the 5′ and 3′ termini (5′-UTR and 3′-UTR), was sequenced. The whole genome of SCMV (on the basis of 10 isolates) is 9610 nt long, including the 3′ and 5′ termini, and contains a single large open reading frame (ORF). Recombination events in the concatenated sequences of each SCMV isolate were identified by RDP3. Only the events supported by at least 5 different RDP3-implemented methods were considered and shown here. The 15 long light blue bars stand for the complete genomes of 15 recombinants while the 20 gray areas in the light blue bars represent regions substituted from another virus strain, identity thereof given by the 20 short differently colored bars corresponding to the gray areas.

Fig 2. Neighbor-joining tree based on the genome sequences of Sugarcane mosaic virus.

Bootstrap analysis was applied using 1000 replicates. Only bootstrap values (%) higher than 70 are given. Potato virus Y was used as the outgroup.