Genome-wide identification and characterization of microsatellite markers within the Avipoxviruses

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.

Genome-wide mining and comparative analysis of microsatellite markers fromOrientia tsutsugamushigenomes

“…Microsatellites have been shown to play a key role in transcription, protein function and gene regulation (Kashi, Y. et al, 2007) and utilized as a biomarker for population genetics, linkage association studies (Usdin, K et al, 2008). Escherichia coli (E. coli) microsatellites have been extensively studied in prokaryotic genome (Chen et al, 2011), then after the distribution, polymorphism and characterization of microsatellite have been studied in various prokaryotic and eukaryotic genomes, including Burkholderia pseudomallei (Ledenyova et al, 2019), Hemopillus influenza (Power et al, 2009), Lactobacillus (Basharat et al, 2015), Mycobacterium tuberculosis (Sreenu et al, 2006), Mycobacterium bovis (Sreenu et al, 2006), Saccharomyces cerevisiae (Bagshaw A et al, 2008) and DNA viruses such as Human papilloma virus (HPV) (Chen et al, 2012), Adenovirus (Houng et al, 2009), ORF virus (Sahu et al, 2020), Avipoxvirus (Sahu et al, 2022), also in RNA viruses like HIV (Chen et al, 2012), tobamovirus (Alam CM et l., 2013), Carlavirus (Alam CM et al, 2014). Here we investigated the comparative analysis, distribution, and characterization of microsatellites in nine complete OT genomes, which have one of the most complex genomes to date and can serve as an ideal model organism for studying the nature of microsatellites.…”

“…Mycobacterium bovis (Sreenu et al, 2006), Saccharomyces cerevisiae and DNA viruses such as Human papilloma virus (HPV) (Chen et al, 2012), Adenovirus (Houng et al, 2009), ORF virus (Sahu et al, 2020), Avipoxvirus (Sahu et al, 2022), also in RNA viruses like HIV (Chen et al, 2012), tobamovirus (Alam CM et l., 2013), Carlavirus . Here we investigated the comparative analysis, distribution, and characterization of microsatellites in nine complete OT genomes, which have one of the most complex genomes to date and can serve as an ideal model organism for studying the nature of microsatellites.…”

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

“…Comparative genome mapping is one of the important applications for microsatellite mining (Sharma, Grover et al 2007). Till now, systematic analysis with regard to microsatellite abundance, distribution, differentiation, and characterization have been accomplished on humans (Eckert and Hile 2009), primates (Xu, Li et al 2018), plants (Kalia, Rai et al 2011), fungi (Oliveira and Azevedo 2022), viruses (Sahu, Majee et al 2020, Sahu, Majee et al 2022), and bacteria (Panda, Swain et al 2023). By implementing comparative genomics approaches between pigs, cattle, and humans, interspecific microsatellite markers were developed (Sun and Kirkpatrick 1996).…”

Microsatellite Density Landscapes Illustrate Short Tandem Repeats Aggregation in The Complete Reference Human Genome

“…And microsatellites of human sequences comprised of GA/TC/GC/AT bases are investigated using seq-requester microsatellite (Nurk et al 2022). However, we applied a threshold of 6, 3, 3, 3, 3, 3 iterations for mono-to hexa-nucleotide repeat motifs for analyzing microsatellites in the complete reference human genome T2T-CHM13, the threshold was widely used to study microsatellites in the genome sequences of viruses, mitochondrial and chloroplast (Chen et al 2010;Zhao et al 2012;de Freitas et al 2022;Sahu et al 2022).…”

“…And microsatellites of human sequences comprised of GA/TC/GC/AT bases are investigated using seq-requester microsatellite (Nurk et al 2022). However, we applied a threshold of 6, 3, 3, 3, 3, 3 iterations for mono- to hexa-nucleotide repeat motifs for analyzing microsatellites in the complete reference human genome T2T-CHM13, the threshold was widely used to study microsatellites in the genome sequences of viruses, mitochondrial and chloroplast (Chen et al 2010; Zhao et al 2012; de Freitas et al 2022; Sahu et al 2022). And we have first applied the threshold to investigate microsatellites in the Y-DNA of the human reference genome (GRCh38, NC_000024.10) at 1 Kbp resolution by Differential Calculator of Microsatellite version 2.0 (DCM 2.0) method, revealing an exact distributional feature of STRs in every local bins of 1 Kbp sequence of the chromosome Y (Li et al 2021).…”