Phylogenetic analysis and signature of recombination hotspots in sugarcane mosaic virus infecting sugarcane in India

Ultrasensitive nano-gold labelled, duplex lateral flow immunochromatographic assay for early detection of sugarcane mosaic viruses

Sugarcane is one of the important food and bioenergy crops, cultivated all over the world except European continent. Like many other crops, sugarcane production and quality are hampered by various plant pathogens, among them viruses that infect systemically and cause severe impact to cane growth. The viruses are efficiently managed by their elimination through tissue culture combined with molecular diagnostics, which could detect virus titre often low at 10^-12 g mL^-1. To harmonize the virus diagnostics by molecular methods, we established a nanocatalysis-based high sensitive lateral flow immunochromatographic assay (LFIA) simultaneously to detect two major sugarcane viruses associated with mosaic disease in sugarcane. LFIA is known for poor sensitivity and stability with its signalling conjugates. However, we synthesized positively charged Cysteamine-gold nanoparticles and used them to prepare highly stable to sensitive immunoconjugates and as a colourimetric detection label. Further nanogold signal enhancement was performed on LFIA to obtain a high detection sensitivity, which is higher than the conventional immunoassays. The linear detection range of the nano-LIFA was 10^-6 to 10^-9 g mL^-1, and with the signal enhancement, the LOD reached up to 10^-12 g ml^-1. This research paper provides relative merits and advancement on nano-LFIA for specific detection of sugarcane viruses in sugarcane for the first time.

The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species

Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV.

Sugarcane Mosaic Disease: Characteristics, Identification and Control

Mosaic is one of the most important sugarcane diseases, caused by single or compound infection of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and/or Sugarcane streak mosaic virus (SCSMV). The compound infection of mosaic has become increasingly serious in the last few years. The disease directly affects the photosynthesis and growth of sugarcane, leading to a significant decrease in cane yield and sucrose content, and thus serious economic losses. This review covers four aspects of sugarcane mosaic disease management: first, the current situation of sugarcane mosaic disease and its epidemic characteristics; second, the pathogenicity and genetic diversity of the three viruses; third, the identification methods of mosaic and its pathogen species; and fourth, the prevention and control measures for sugarcane mosaic disease and potential future research focus. The review is expected to provide scientific literature and guidance for the effective prevention and control of mosaic through resistance breeding in sugarcane.

Identification of the RNA silencing suppressor activity of sugarcane streak mosaic virus P1 gene

Sugarcane streak mosaic virus (SCSMV) belonging to Poacevirus, is a causative virus of mosaic disease in sugarcane in many Asian countries with substantial genomic variation. Although the virus infects the crop with Sugarcane mosaic virus (SCMV) a Potyvirus, it predominates over SCMV in spread as well as titre. We have taken up detailed studies to identify the functional activity of viral suppressors of SCSMV genome. Transient expression assay was performed with SCSMV-P1 and HC-Pro genes in the model plant Nicotiana tabacum to establish suppressor role of these genes. The plasmid constructs of both the genes were co-infiltrated with the reporter green fluorescent protein (GFP) and the suppressor activity was measured as enhancement in the GFP fluorescence. Further, the phenotypic expressions were validated by respective gene expression through semi quantitative and qRT-PCR. In the P1 co-infiltrated GFP leaves, suppression in the PTGS mechanism took place that allowed a long term expression of GFP. However, GFP co-infiltrated with HC-Pro did not sustain the GFP expression level for a prolonged period and the expression level was close to GFP control. The study concluded that unlike in other Potyviridae genera, P1 gene of SCSMV is playing the role of RNA silencing suppressor. This study helps in unveiling a new and promising way to understand the regulatory pathway in the host at the time of viral infection. Targeting the P1 gene of SCSMV through RNA silencing approach will be a viable strategy to develop mosaic resistant transgenic sugarcane varieties as they are directly involved in counter defence against the host.

Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences

Sugarcane mosaic virus (SCMV), a member of the genus Potyvirus in the family Potyviridae, is an important pathogen that causes mosaic diseases in maize, sugarcane, canna and other graminaceous species worldwide. Previously, several reports have showed the genetic variation and population structure of SCMV. However, the evolutionary dynamics, synonymous codon usage pattern and adaptive evolution of the virus is unclear. In this study, we performed comprehensive analyses of phylodynamics, composition bias and codon usage of SCMV using 108 complete genomic sequences. Our phylogenetic analysis found six host- and geographically confined phylogenetic lineages within the SCMV non-recombinant isolates. We found a relatively stable and conserved genomic composition with a lower codon usage choice in the SCMV protein coding sequences. Mutation pressure and natural selection have shaped the codon usage patterns of the SCMV protein coding sequences with natural selection being the dominant factor. The codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses revealed a stronger correlation between SCMV and maize than between SCMV and sugarcane or canna. Our study is the first to evaluate the codon usage pattern of SCMV based on complete sequences and may provide a better understanding of the origin of SCMV and its evolutionary patterns for future research.