Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes

Comprehensive Comparative Analysis Sheds Light on the Patterns of Microsatellite Distribution across Birds Based on the Chromosome-Level Genomes

Microsatellites (SSRs) are widely distributed in the genomes of organisms and are an important genetic basis for genome evolution and phenotypic adaptation. Although the distribution patterns of microsatellites have been investigated in many phylogenetic lineages, they remain unclear within the morphologically and physiologically diverse avian clades. Here, based on high-quality chromosome-level genomes, we examined the microsatellite distribution patterns for 53 birds from 16 orders. The results demonstrated that each type of SSR had the same ratio between taxa. For example, the frequency of imperfect SSRs (I-SSRs) was 69.90-84.61%, while perfect SSRs (P-SSRs) were 14.86-28.13% and compound SSRs (C-SSRs) were 0.39-2.24%. Mononucleotide SSRs were dominant for perfect SSRs (32.66-76.48%) in most bird species (98.11%), and A(n) was the most abundant repeat motifs of P-SSRs in all birds (5.42-68.22%). Our study further confirmed that the abundance and diversity of microsatellites were less effected by evolutionary history but its length. The number of P-SSRs decreased with increasing repeat times, and longer P-SSRs motifs had a higher variability coefficient of the repeat copy number and lower diversity, indicating that longer motifs tended to have more stable preferences in avian genomes. We also found that P-SSRs were mainly distributed at the gene ends, and the functional annotation for these genes demonstrated that they were related to signal transduction and cellular process. In conclusion, our research provided avian SSR distribution patterns, which will help to explore the genetic basis for phenotypic diversity in birds.

Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families

Microsatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Circoviridae, and Parvoviridae, known to predominantly infect livestock and humans. Among these virus families, 0-58.49% of perfect microsatellites were involved in the formation of compound microsatellites, the majority being located in the coding regions. No clear relationship existed between the genomic features (genome size and GC%) and compound microsatellite characteristics (relative abundance and relative density). The majority of the compound microsatellites resulted from di-SSR couples. A strong positive relationship was observed between the maximum distance value and length of compound microsatellite, percentage of microsatellites involved in the compound microsatellite formation, and relative microsatellite density. The degree of variability among microsatellite characteristics studied was largely a species-specific phenomenon. A major proportion of compound microsatellites was represented by similar motif combinations. The findings of the present study will help in better understanding of the structural, functional, and evolutionary role of compound microsatellites prevailing in the smaller genomes.

Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome

Genome-wide in-silico identification of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036-1,181 microsatellites per strain. The further screening revealed the presence of 83-107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6-8.4 and 53.0-59.5 bp/kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6-0.8 and 12.1-17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD significantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-significantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)-x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. Finally, in-silico polymorphism was assessed, followed by in-vitro validation using PCR analysis and sequencing. The thirteen polymorphic SSR markers developed in this study were further characterized by mapping with the sequence present in the database. The results of the present study indicate that these SSRs could be a useful tool for identification, analysis of genetic diversity, and understanding the evolutionary status of the virus.

Pin1 liberates the human immunodeficiency virus type-1 (HIV-1): Must we stop it?

Acquired immune deficiency syndrome (AIDS) is mainly caused by the human immunodeficiency virus type-1 (HIV-1). To our knowledge, this is the first review focusing on the vital role of Pin1 in the infection of HIV-1 and the development of AIDS. We and others have demonstrated that Pin1, the only known cis-to-trans isomerase recognizing the pThr/pSer-Pro motifs in proteins, plays striking roles in several human diseases. Interestingly, recent evidence gradually indicates that Pin1 regulates several key steps of the life cycle of HIV-1, including the uncoating of the HIV-1 core, the reverse transcription of the RNA genome of HIV-1, and the integration of the HIV-1 cDNA into human chromosomes. Whereas inhibiting Pin1 suppresses all of these key steps and attenuates the replication of HIV-1, at the same time different PIN1 gene variants are correlated with the susceptibility to HIV-1 infection. Furthermore, Pin1 potentially promotes HIV-1 infection by activating multiple oncogenes and inactivating multiple tumor suppressors, extending the life span of HIV-infected cells. These descriptions suggest Pin1 as a promising therapeutic target for the prevention of HIV-1 and highlight the possibility of blocking the development of AIDS by Pin1 inhibitors.

In- silico exploration of thirty alphavirus genomes for analysis of the simple sequence repeats

The compilation of simple sequence repeats (SSRs) in viruses and its analysis with reference to incidence, distribution and variation would be instrumental in understanding the functional and evolutionary aspects of repeat sequences. Present study encompasses the analysis of SSRs across 30 species of alphaviruses. The full length genome sequences, assessed from NCBI were used for extraction and analysis of repeat sequences using IMEx software. The repeats of different motif sizes (mono- to penta-nucleotide) observed therein exhibited variable incidence across the species. Expectedly, mononucleotide A/T was the most prevalent followed by dinucleotide AG/GA and trinucleotide AAG/GAA in these genomes. The conversion of SSRs to imperfect microsatellite or compound microsatellite (cSSR) is low. cSSR, primarily constituted by variant motifs accounted for up to 12.5% of the SSRs. Interestingly, seven species lacked cSSR in their genomes. However, the SSR and cSSR are predominantly localized to the coding region ORFs for non structural protein and structural proteins. The relative frequencies of different classes of simple and compound microsatellites within and across genomes have been highlighted.

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This is the first analysis of SSR and cSSR in alphaviruses.

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We analysed differential frequency and distribution patterns of SSRs and cSSRs.

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We studied localization of SSR and cSSR in alphaviruses proteomics

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This study would help in better understanding of evolutionary biology of alphaviruses.

Genome wide survey and analysis of small repetitive sequences in caulimoviruses

Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life including viruses. Members of the Caulimoviridae family severely affect growth of vegetable and fruit plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 44 species of Caulimoviridae. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, mono- and dinucleotide repeats were found to be highly predominant and are overrepresented in genome of majority of caulimoviruses. AT/TA and GAA/AAG/AGA was the most abundant di- and trinucleotide repeat motif, respectively. Repeats larger than trinucleotide were rarely found in these genomes. Comparative study of occurrence, abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were least abundant in genomes of caulimoviruses. Polymorphic repeats even though rare were observed in the large intergenic region of the genome, indicating strand slippage and/or unequal recombination processes do occur in caulimoviruses. To our knowledge, this is the first analysis of microsatellites occurring in any dsDNA viral genome. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.