Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes.
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ABSTRACT:
SUBMITTER: Siddiqe R
PROVIDER: S-EPMC7835092 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundMicrosatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars.ObjectiveThis is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species.MethodsWe identified and compared perfect SSRs with 1-6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, Elaeis oleifera, and Elaeis guineensis.ResultsA total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs.ConclusionWe envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes.
| S-EPMC7181556 | biostudies-literature
Project description:Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1-4 bp length, designated LSSR(1-4)) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5-11 bp length, designated LSSR(5-11)) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR(1-4) are likely maintained by selection. This is consistent with the established role of some LSSR(1-4) in enhancing antigenic variance. By contrast, abundance of LSSR(5-11) in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed.
| S-EPMC1895974 | biostudies-literature
Project description: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.
| S-EPMC4287844 | biostudies-literature
Project description:BackgroundHepatitis E virus (HEV) is small (27-34 nm diameter) non-enveloped with positive sense ssRNA genome. Microsatellites or simple sequence repeats (SSR) are short tandem repeat sequences present across coding and non-coding regions of both prokaryotes and eukaryotes. They are involved with genome function and evolution at multiple levels.ResultsThe complete genome sequences of 22 HEV genomes of the family Hepeviridae and genus Orthohepevirus (21 species) and Piscihepevirus (1 species) were extracted from NCBI database ( http://www.ncbi.nlm.nih.gov/ ). The extraction of microsatellites was done using Imperfect Microsatellite Extractor (IMEx) in 'Advance-Mode'. The average genome size of the studied HEV genomes was 7003nt and it ranged from 6649nt (HEV11) to 7310nt (HEV22). The average GC content of the genomes was ~ 55%. A total of 519 SSRs and 21 cSSRS were extracted from the HEV genomes with an average incidence of 24 per genome ranging from 14 (HEV13) to 34 (HEV19). The cSSR incidence ranged from 0 (eight species) to 4 (HEV19). The genomes with no cSSR incidence had an SSR incidence range from 14 to 28. There were just four hexa-nucleotide repeat motifs and 5 penta-nucleotide repeat motifs observed. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were "C", "GT/TG", and "GAC/CTG" respectively. The studied genomes had a minimum of ~ 90% incident SSRs present in the coding regions. Viruses with same or similar hosts are placed together on the phylogenetic tree implicating viral host being one of the driving forces for evolution. Conclusions Host range in viruses is being decided by multiple factors aided by the unique genome SSR signature and genomes of varied compositions need to be analyzed to forge a widely acceptable rule for predicting the same.
| S-EPMC9114184 | biostudies-literature
Project description:Staphylococci are Gram-positive bacteria which play an important role in infectious disease and are major causes of communityacquired and hospital-acquired infections. Strains of Staphylococcus aureus are reported as genomically and phenotypically highly heterogeneous; hence in-silico based comparison of genomic data on simple sequence repeats may provide valuable information for understanding the pathogenicity and control measures. This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of six Staphylococcus strains (Staphylococcus aureus COL, S.aureus MRSA252, S.aureus MSSA476, S.aureus Mu50, S.aureus MW2, S.aureus N315) and plasmid sequences of four Staphylococcus strains (Staphylococcus aureus COL pT181, Staphylococcus aureus MSSA pSAS, Staphylococcus aureus VRSAp, Staphylococcus aureus, Staphylococcus aureus pN315 DNA) downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study shows that (i) a large number of tandem repeats are distributed throughout the genome and plasmid sequences. (ii) Number of mononucleotide SSRs decreased rapidly with increase in size of repeat unit. (iii) Total frequency of SSRs in plasmid regions is less than genomic regions. (iv) In all investigated strains, ratios of AT/TA repeats are dominating over GC/CG repeats in genomics as well as plasmid sequences, and (v) Dinucleotide combination of AT is dominated in all the six Staphylococcus genome sequences.
| S-EPMC3530869 | biostudies-literature
Project description:UnlabelledComputational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes.AbbreviationsSSRs - Simple Sequence Repeats, ORFs - Open Reading Frames.
| S-EPMC3124796 | biostudies-literature
Project description:Bitter gourd (Momordica charantia) is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo) genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs) in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines 'Dali-11' and 'OHB3-1,' respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines 'Dali-11' and 'K44'. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.
| S-EPMC5479929 | biostudies-literature
Project description:BackgroundCucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.ResultsA total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.ConclusionsThe cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
| S-EPMC3091718 | biostudies-literature
Project description: Not available
| S-BSST1334 | biostudies-other
Project description:We present a detailed genome-scale comparative analysis of simple sequence repeats within protein coding regions among 25 insect genomes. The repetitive sequences in the coding regions primarily represented single codon repeats and codon pair repeats. The CAG triplet is highly repetitive in the coding regions of insect genomes. It is frequently paired with the synonymous codon CAA to code for polyglutamine repeats. The codon pairs that are least repetitive code for polyalanine repeats. The frequency of hexanucleotide and dinucleotide motifs of codon pair repeats is significantly (p<0.001) different in the Drosophila species compared to the non-Drosophila species. However, the frequency of synonymous and non-synonymous codon pair repeats varies in a correlated manner (r(2)=0.79) among all the species. Results further show that perfect and imperfect repeats have significant association with the trinucleotide and hexanucleotide coding repeats in most of these insects. However, only select species show significant association between the numbers of perfect/imperfect hexamers and repeat coding for single amino acid/amino acid pair runs. Our data further suggests that genes containing simple sequence coding repeats may be under negative selection as they tend to be poorly conserved across species. The sequences of coding repeats of orthologous genes vary according to the known phylogeny among the species. In conclusion, the study shows that simple sequence coding repeats are important features of genome diversity among insects.
| S-EPMC3383938 | biostudies-literature