Abstract
In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN–1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions. Among the 39 motifs located in coding regions, 21 were located in annotated functional genes whilst 18 were identified in unknown functional genes (hypothetical proteins). Among the identified motifs, trinucleotide (80%) repeats were found to be the most abundant followed by dinucleotide (13%), mononucleotide (5%) and hexanucleotide (2%) repeats. The 39 motifs located within coding regions were further validated in vitro by using PCR analysis, while the 21 motifs located within known functional genes (15 genes) were characterized using nucleotide sequencing. A comparison of the sequence analysis data of the 21 sequenced cSSRs with the published sequences is presented. Finally, the developed SSR markers of the 39 motifs were further mapped/localized onto the SpliMNPV-AN1956 genome. In conclusion, the SSR markers specific to SpliMNPV, developed in this study, could be a useful tool for the identification of isolates and analysis of genetic diversity and viral evolutionary status.
Highlights
Sequencing, DNA restriction analysis and molecular phylogeny, several new and highly useful tools for gene and genome characterization are accessible to us
Assessing the relative composition of the repeat types within the covered ORFs revealed that the 38 cSSRs (97.4%) concerned were predominantly composed of trinucleotide repeats with only one mononucleotide motif (2.6%) identified
We have identified and characterized 39 cSSRs from a total of 55 Simple sequence repeats (SSRs) motifs distributed within the SpliMNPV genome
Summary
Sequencing, DNA restriction analysis and molecular phylogeny, several new and highly useful tools for gene and genome characterization are accessible to us. SSRs are found in a variety of genomic regions including the 3′and 5′untranslated regions as well as exons and introns (protein-coding and non-coding regions)[8,9,10] For this reason, SSRs are speculated to play a variety of diverse roles in the eukaryotic, prokaryotic and viral genomes. Despite the growing number of completely sequenced viral genomes submitted to the public database, little attention has been paid towards surveying SSRs at the genome level for viruses in general and baculoviral genomes in particular. In spite of their abundance and functional relevance in viral genomes, the distribution pattern of microsatellites remains to be fully elucidated[7]. We propose that the results have the potential to expand our understanding of virus diversity, evolution and isolate identification
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