Article3 Biotech2022
Genome-wide identification and characterization of microsatellite markers within the Avipoxviruses.
Article in 3 Biotech, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 6 citations in OpenAlex.
- Enrichment and Reduction of Microsatellite Regions in the Myxoma Virus Genome Following Species Jump to the Iberian Hare (Transboundary and emerging diseases · 2026Article
- Genome-Wide Microsatellites inAnimals : an open access journal from MDPI · 2024Article
- Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome.BMC genomics · 2024Article
- Insights into genome plasticity and gene regulation in3 Biotech · 2023Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microsatellite markers or Simple Sequence Repeats (SSRs) are gaining importance for molecular characterization of the virus as well as estimation of evolution patterns due to its high-polymorphic nature. The Avipoxvirus is the causative agent of pox-like lesions in more than 300 birds and one of the major diseases for the extinction of endangered avian species. Therefore, we conducted a genome-wide analysis to decipher the type, distribution pattern of 14 complete genomes derived from the Avipoxvirus genus. The in-silico screening deciphered the existence of 917-2632 SSRs per strain. In the case of compound SSRs (cSSRs), the value was obtained 44-255 per genome. Our analysis indicates that the di-nucleotide repeats (52.74%) are the most abundant, followed by the mononucleotides (34.79), trinucleotides (11.57%), tetranucleotides (0.64%), pentanucleotides (0.12%) and hexanucleotides (0.15%) repeats. The specific parameters like Relative Abundance (RA) and Relative Density (RD) of microsatellites ranged within 5.5-8.12 and 33.08-53.58 bp/kb. The analysis of RA and RD value of compound microsatellites resulted between 0.25-0.82 and 4.64-15.12 bp/kb. The analysis of motif composition of cSSR revealed that most of the compound microsatellites were made up of two microsatellites, with some unique duplicated pattern of the motif like, (TA)-x-(TA), (TCA)-x-(TCA), etc. and self-complementary motifs, such as (TA)-x-(AT). Finally, we validated forty sets of compound microsatellite markers through an in-vitro approach utilizing clinical specimens and mapping the sequencing products with the database through comparative genomics approaches. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03169-4.
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