Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

Abstract

Background:Microsatellites have evoked the interest of researchers owing to their applications in different fields such as DNA fingerprinting, genetic mapping, population genetics, forensics, paternity studies and evolution. Objectives: The present study focused on the analysis of simple sequence repeats (SSRs) in genomes of seven species from three genera of the Filoviridae family. Materials and Methods: Genome sequences of seven species from the Filoviridae family were assessed by the National Center for Biotechnology Information (NCBI), microsatellites were extracted using the IMEx software, and statistical analysis was performed Microsoft Office Excel 2007. Results: A total of 516 microsatellites and 14 Compound Simple Sequence Repeats (cSSR) (also known as compound microsatellites) were extracted. Evidently, the conversion of SSRs to cSSR was low. Mononucleotide A/T was the most prevalent followed by dinucleotide AC/CA and trinucleotide AAC/CAA. Highest incidence of SSRs (mon-/di-nucleotide motif) was observed in RNA Dependent RNA Polymerase (RDRP) gene whereas tri-nucleotide motif was maximally localized in nucleoproteins (NP). Conclusions:The salient features of simple and compound microsatellites in Filoviridae family have been highlighted herein. Microsatellite regions with higher mutation rates compared to the rest of the genome play a crucial role in genome evolution by acting as a source of quantitative genetic variation. The SSR mutation rate is known to be affected by motif length, motif sequence, and number of repeats and purity of repetition. The functional role of tandem repeats in viruses, remains to be fully elucidated. However, with the repetitive sequence allegedly acting as a hot spot for recombination, we postulate their involvement in genetic events such as recombination, replication, and repair mechanisms that drive sequence diversity leading to the formation of the genetic basis of adaptation.

Conserved microsatellites may contribute to stem-loop structures in 5′, 3′ terminals of Ebolavirus genomes

“…Microsatellites were previously reported to be more abundant in noncoding regions [29,47]. According to statistics, except for the longest L gene, the microsatellites in the non-coding regions of Ebolavirus are the most [20]. However, in this research, the variances of the terminal sequences were clearly more than other sequences in Ebolavirus genomes.…”

“…The distribution of microsatellites on Ebolavirus genomes had regional preference between and among species [20]. Due to the isolation of many viruses still require the differentiation of thousands of years [46], the viral genome often produces more mutations.…”

“…Microsatellites might potentially contribute to evolution of virus, through the comprehensive analysis of viral genomes in HIV-1 [17], Potyvirus [18] and HCV [19]. The distribution and composition of microsatellites in seven species of Filoviridae family, including Ebolavirus, also have salient features [20]. Ebolavirus comprises of five species: Zaire ebolavirus, Bundibugyo virus, Reston ebolavirus, Sudan ebolavirus, and Taï Forest ebolavirus [21].…”

“…It is organized into a 3 0 leader non-coding regions, followed by seven genes and a 5 0 trailer non-coding regions [22]. Microsatellites in non-coding regions account for a large proportion of the Ebolavirus genomes [20].…”

Duplicates, redundancies, and inconsistencies in the primary nucleotide databases: a descriptive study

“…Overall, other than the Exact fragments and Similar fragments categories, the majority of the remainder has differences of GC content and melting temperature of over 0.1°C. Many studies report these values to three digits of precision, or even more (57)(58)(59)(60)(61)(62). The presence of duplicates means that these values in fact have considerable uncertainty.…”