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

Abstract

BackgroundSugarcane 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.ResultsDouble-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.ConclusionsNegative 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.

Detección del Virus del mosaico de la caña de azúcar (SCMV) en Saccharum spp. en México y origen filogenético de un aislado de Jalisco

“…However, due to the number of HCPro sequences of SCMV, it is very reduced in the NCBI data base in comparison with the CP sequences, it was not possible to relate the origin of the Mexican isolation with important sugarcane producing countries such as Brazil, United States, Colombia, and others. In this study we obtained the formation of two groups based on partial HCPro sequences of SCMV, and this same tendency was previously reported by Chaves and Ortiz (2012) and Xie et al (2016), using CP sequences of SCMV. Similarly, these authors coincide in that the formation of these groups is related to the hosts of SCMV: sugarcane and maize, mainly.…”

“…Sin embargo, debido a que el número de secuencias HC-Pro del SCMV es muy reducido en la base de datos de NCBI a comparación del número de secuencias CP, no fue posible relacionar el origen del aislado mexicano con países cañeros importantes como Brasil, Estados Unidos, Colombia, entre otros. En este estudio se obtuvo la formación de dos grupos basados en secuencias parciales HC-Pro de SCMV, esta misma tendencia fue reportada previamente por Chaves y Ortiz (2012) y Xie et al (2016), utilizando secuencias CP de SCMV. De forma similar, estos autores coinciden que la formación de estos grupos está asociada con los hospederos que tiene el SCMV: caña de azúcar y maíz, principalmente.…”

“…En el año 2012 se reportó un análisis filogenético de 185 secuencias CP del SCMV provenientes de varios países, sugiriendo diferentes orígenes filogeográfi-cos de dos aislados mexicanos que contemplo ese estudio (Chaves y Ortiz, 2012). Por otra parte, los resultados de Xie et al (2016) del análisis filogenético de 24 aislados de SCMV provenientes de China y diversos países del mundo revelaron que podrían dividirse en dos grupos, los cuales fueron asociados con la especie vegetal hospedera del SCMV. Más recientemente, los resultados de Moradi et al (2017) a partir de secuencias CP del SCMV de Filippone et al (2010) optimized a protocol to detect SCMV using the oligonucleotides described earlier by Yang by Mirkov (1997) and Smith and Van de Velde (1994), respectively.…”

“…In the year 2012, a phylogenetic analysis was reported, with 185 SCMV CP sequences from several countries, suggesting different phylogeographic origins of two Mexican isolates that this study considered (Chaves and Ortiz, 2012). On the other hand, the results produced by Xie et al (2016) on the phylogenetic analysis of 24 SCMV isolates from China and other countries revealed that they could be divided into two groups, which were related to the SCMV host plant species. More recently, results by Moradi et al (2017) from CP sequences of SCMV from various countries suggest five divergent evolutionary lineages, where the geographic origin and/or SCMV host plants are partially related.…”

Detection and Response of Sugarcane against the Infection of Sugarcane Mosaic Virus (SCMV) in Indonesia

“…Many researchers have used several tools to detect these pathogens by examining virus particles using electron microscopy [26], enzyme-linked immunosorbant assay (ELISA) [11], or by reverse transcriptase polymerase chain reaction (RT-PCR) [20] combined with DNA sequencing, particularly on the coat protein gene fragment. The sequence of the coat protein gene for SCMV is commonly used to identifying mosaic pathogens, for instance the identification of mosaic disease on sugarcane and maize in Thailand [27], maize and canna in China [28][29][30][31], and sugarcane in Argentina [32]. Moreover, according to the coat protein sequence, the virus is also easily grouped into strain, because the sequence has unique parts among strains of SCMV related to their hosts [28], and more specifically, it has unique parts at the N-terminal amino acid residue of coat protein which is the second trypsin cleavage site and the residues which contain repeat sequence motifs [27].…”