Compound Microsatellites Research Articles

Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes

Simple sequence repeats (SSRs) are tandem-repeated sequences ubiquitously present but differentially distributed across genomes. Present study is a systematic analysis for incidence, composition and complexity of different microsatellites in 48 representative Human papillomavirus (HPV) genomes. The analysis revealed a total of 1868 SSRs and 120 cSSRs. However, four genomes (HPV-60, HPV-92, HPV-112 and HPV-136) lacked any cSSR content; while HPV-31 accounted for a maximum of 10 cSSRs. An overall increase in cSSR% with higher dMAX was observed. The SSRs and cSSRs were prevalent in coding regions. Poly(A/T) repeats were significantly more abundant than poly(G/C) repeats possibly due to high (A/T) content of the HPV genomes. Further, higher prevalence of di-nucleotide repeats over tri-nucleotide repeats may be attributed to instability of former because of higher slippage rate. An in-depth study of the satellite sequences would provide an insight into the imperfections and evolution of microsatellites.

Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses

An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences.

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent

BackgroundMicrosatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.DescriptionFishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview.ConclusionsFishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

An in-silico analysis of simple sequence repeats (SSRs) in 30 species of tobamoviruses was done. SSRs (mono to hexa) were present with variant frequency across species. Compound microsatellites, primarily of variant motifs accounted for up to 11.43% of the SSRs. Motif duplications were observed for A, T, AT, and ACA repeats. (AG)–(TC) was the most prevalent SSR-couple. SSRs were differentially localized in the coding region with ~54% on the 128kDa protein while 20.37% was exclusive to 186kDa protein. Characterization of such variations is important for elucidating the origin, sequence variations, and structure of these widely used, but incompletely understood sequences.

Development of microsatellite markers in sweet passion fruit, and identification of length and conformation polymorphisms within repeat sequences

AbstractThe aim of this study was to construct and characterize an SSR‐enriched genomic library for Passiflora alata, a fruit species native to the Brazilian plateau and the eastern Amazon region. There is potential to improve this crop, as the fruit is attractive because of its pleasant aroma and flavour characteristics. Of 862 sequences, 391 (45%) were found to have SSRs. We identified 412 microsatellites: 69% were classified as perfect, 23% imperfect, 5% interrupted and 3% were compound microsatellites. The main types of repeat sequences were dinucleotide (62.5%) and trinucleotide (23%) repeats. It was possible to design 312 primer pairs, and 229 of them were synthesized and tested. The amplicons were electrophoresed using denaturing and non‐denaturing gels to screen for divergence between two phenotypically distinct parents of a mapping population of P. alata. Length and conformation polymorphisms within repeat sequences amounted to 35% and 28%, respectively. The importance of the development of SSR markers for sweet passion fruit and the effectiveness of the SSCP approach to increase the available number of polymorphic SSRs are discussed.

Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes

Simple sequence repeats (SSRs) or microsatellites are known to exhibit ubiquitous across all kingdoms of life including viruses. However, imperfections in simple sequence repeats have been analyzed in genomes of human, Escherichia coli and Human Immunodeficiency virus. The assessment of compound microsatellites in plant viral genomes is yet to be studied. Potyviruses severely affect crop plant growth and reduce economic yield in diverse cropping systems worldwide. Hence, we analyze the nature and distribution of compound microsatellites present in complete genome of 45 potyvirus species. The results indicate that compound microsatellites accounted for about 0% to 15.15% of all microsatellites and have low complexity as compared to that of prokaryotic genomes. Overall, 14% of compound microsatellites were of similar motifs and such motif duplications were observed for CA, TA and AG repeats. Among all 45 potyvirus genomes analyzed, SSR couple (AG)-x-(AC) was found to be the most abundant one. Hence it is apparent that in contrast to eukaryotes, majority of compound microsatellites in potyviruses were composed of variant motifs. We also highlight the relative frequency of different classes of compound microsatellites as well as their patterns of distribution and correlate with biology of potyviruses. Further characterization of such variation is important for elucidating the origin, mutational processes, and structure of these widely used, but incompletely understood sequences.

MSDB: A User-Friendly Program for Reporting Distribution and Building Databases of Microsatellites from Genome Sequences

Microsatellite Search and Building Database (MSDB) is a new Perl program providing a user-friendly interface for identification and building databases of microsatellites from complete genome sequences. The general aims of MSDB are to use the database to store the information of microsatellites and to facilitate the management, classification, and statistics of microsatellites. A user-friendly interface facilitates the treatment of large datasets. The program is powerful in finding various types of pure, compound, and complex microsatellites from sequences as well as generating a detailed statistical report in worksheet format. MSDB also contains other two subprograms: SWR, which is used to export microsatellites from the database to meet user's requirements, and SWP, which is used to automatically invoke R to draw a sliding window plot for displaying the distribution of density or frequency of identified microsatellites. MSDB is freely available under the GNU General Public license for Windows and Linux from the following website: http://msdb.biosv.com/.

Evaluation of genetic diversity in a Camelina sativa (L.) Crantz collection using microsatellite markers and biochemical traits

A genomic DNA library enriched with GA/TC repeats from Camelina sativa variety Calena has been analysed. After sequencing of about 200 randomly selected clones, approximately 60 % of them showed to contain simple or compound microsatellites with a high number of repeats. Among all microsatellite markers analysed 15 primer pairs amplified polymorphic fragments. Forty C. sativa accessions of different origin were genotyped with 15 microsatellite markers that generated 134 alleles with an average of 8.93 alleles per locus. The observed heterozygosity (Ho) among the accessions ranged from 0.0 to 0.15 with an average of 0.0370, whereas the average of expected heterozygosity (He) among accessions was 0.2769. The analysis of the average total heterozygosity (HT = 0.651), the intrapopulation genetic diversity (HS = 0.260), the interpopulation genetic diversity (DST = 0.391) and the coefficient of genetic differentiation among populations (GST = 0.574) demonstrated that 57.4 % of the genetic diversity is among the accessions, while 42.6 % resides within them. Phylogenetic tree of the 40 C. sativa accessions was constructed based on Nei’s genetic distance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram shows, except for CAM108 and CAM170, a clear discrimination among C. sativa accessions grouping them in five subgroups. ANOVA analysis indicates significant differences in some biochemical and agronomic parameters among the C. sativa accessions grouped according to Nei’s genetic distance. The result of the Tukey HSD test demonstrated that the A4 subgroup showed a significant higher TWS and linoleic acid (LA) content, while the subgroup A1 showed a significant higher linolenic and lower LA content compared to the remaining groups.

Differential distribution of compound microsatellites in various Human Immunodeficiency Virus Type 1 complete genomes

Compound microsatellites consist of two or more individual microsatellites, and may originate from dynamic mutations or imperfection of microsatellites. Previous studies have found microsatellites were present in 81 completed Human Immunodeficiency Virus Type 1 (HIV-1) genomes, suggesting compound microsatellites may exist in viral genomes. However, up to now, compound microsatellites have not been analyzed in any viral genomes. We identified and characterized 238 compound microsatellites in 81 completed HIV-1 genomes. About 0–24.24% of all microsatellites could be categorized as compound microsatellites. Compound microsatellite distribution is very different in two aspects between diverse HIV-1 genomes. First, the number and motifs of compound microsatellites are variable between surveyed genomes. Second, the relative abundance and relative density of compound microsatellites exhibit very significant differences between these surveyed genomes, respectively. The relative abundance and relative density of compound microsatellites were weakly correlated with genome size and microsatellite density. We observed a more dynamic picture of compound microsatellites than previously reported in eukaryotes. This might be attributed to the lack of proofreading in HIV-1 genomes, as it has been demonstrated that the loss of polymerase proofreading activity can greatly enhance the mutation rate of microsatellites.

Genetic population structure of the masked palm civet Paguma larvata, (Carnivora: Viverridae) in Japan, revealed from analysis of newly identified compound microsatellites

The masked palm civet Paguma larvata (Carnivora: Viverridae) in Japan has been phylogeographically considered an introduced species from Taiwan. To reveal the population structures and relationships among the P. larvata populations in Japan, seven compound microsatellite loci were isolated from the genome and genotyped for 287 individuals collected from the field. STRUCTURE analysis and factorial correspondence analysis of genotyping data revealed that animals from Japan were divided into four genetic clusters. Geographic distribution of the genetic clusters partly referred to sampling areas, indicating multiple introductions into distinct areas of Japan or independent founding events leading to the generation of different genetic clusters within introduced populations in Japan. The large genetic differentiation of populations in the Shikoku District from those in other areas within Japan suggests that there were at least two introduction routes into Japan, and a possibility that some founders from areas other than Taiwan were also involved in the introduction into Japan. The genetic variation within Japanese populations were not markedly reduced compared with that of Taiwan. The results indicated that the Japanese populations of P. larvata could have retained moderate genetic diversity during founding events, because of multiple introductions, or a large number or high genetic diversity of founders. Although some individuals in Japan showed a sign of admixture between different clusters, there is no evidence that such an admixture markedly increased the genetic diversity within Japanese populations.

Compound microsatellites in complete Escherichia coli genomes

Compound microsatellites consisting of two or more repeats in close proximity have been found in eukaryotic genomes. So far such compound microsatellites have not been investigated in any prokaryotic genomes. We have therefore examined compound microsatellites in 22 complete genomes of Escherichia coli, which is one of the ideal model organisms to analyze the nature and evolution of prokaryotic compound microsatellites. Our results indicated that about 1.75–2.85% of all microsatellites could be accounted as compound microsatellites with very low complexity, and most compound microsatellites were composed of very different motifs. Compound microsatellites were significantly overrepresented in all surveyed genomes. These results were dramatically different from those in eukaryotes. We discussed the possible reasons for the observed divergence.

G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences.

Microsatellites are ubiquitous short tandem repeats found in all known genomes and are known to play a very important role in various studies and fields including DNA fingerprinting, paternity studies, evolutionary studies, virulence and adaptation of certain bacteria and viruses etc. Due to the sequencing of several genomes and the availability of enormous amounts of sequence data during the past few years, computational studies of microsatellites are of interest for many researchers. In this context, we developed a software tool called Imperfect Microsatellite Extractor (IMEx), to extract perfect, imperfect and compound microsatellites from genome sequences along with their complete statistics. Recently we developed a user-friendly graphical-interface using JAVA for IMEx to be used as a stand-alone software named G-IMEx. G-IMEx takes a nucleotide sequence as an input and the results are produced in both html and text formats. The Linux version of G-IMEx can be downloaded for free from http://www.cdfd.org.in/imex.

Polymorphism of Microsatellite Markers in Papaya (Carica papaya L.)

A set of 81 new microsatellite markers for Carica papaya L. previously identified by data mining using freely available sequence information from Genbank were tested for polymorphism using 30 germplasm accessions from the Papaya Germplasm Bank (PGM) at Embrapa Mandioca e Fruticultura Tropical (CNPMF) and 18 landraces. The data were used to estimate pairwise genetic distances between the genotypes. A neighbor-joining based dendrogram was used to define clusters and infer possible genetic structuring of the collection. Most microsatellites were polymorphic (73%), with an observed number of alleles per locus ranging from one to eleven. The levels of observed and expected heterozygosity for 51 polymorphic loci varied from 0.00 to 0.85 and from 0.08 to 0.82, averaging 0.19 and 0.59, respectively. Forty-four percent of microsatellites showed polymorphism information content (PIC) higher than 0.50. The compound microsatellites seem to be more informative than dinucleotide and trinucleotide repeats in average alleles per locus and PIC. Among dinucleotides, AG/TC or GA/CT repeat motifs exhibited more informativeness than TA/AT, GT/CA and TG/AC repeat motifs. The neighbor-joining analysis based on shared allele distance could differentiate all the papaya accessions and landraces as well as differences in their genetic structure. This set of markers will be useful for examining parentage, inbreeding and population structure in papaya.

Microsatellite loci in the carcinogenic liver fluke, Opisthorchis viverrini and their application as population genetic markers

Opisthorchis viverrini is a carcinogenic foodborne trematode endemic in Southeast Asia especially in Thailand and the Lao People's Democratic Republic. Opisthorchiasis causes hepatobiliary diseases and cholangiocarcinoma (bile duct cancer). Currently there is substantial evidence on genetic variation of O. viverrini but the information on population genetic structure is lacking. Because microsatellite DNA of this parasite is not available, we for the first time isolated and utilized microsatellite DNA as genetic markers to examine genetic diversity and the population structure of O. viverrini. Partial genomic DNA libraries were constructed by conventional and enrichment methods which yielded microsatellite-containing clones of 0.18–0.25% and 16.84%, respectively. Within 41 microsatellite loci isolated 36.59% were perfect, 60.98% were interrupted and 2.44% were compound microsatellites. The CA repetitions were the most frequent, followed by GT and CAT. Primers specific to the flanking regions of 12 microsatellite loci were developed to genotype 150 O. viverrini individuals from geographical localities in Thailand and Lao PDR. Allele numbers per locus ranged from 2 to 15, with the mean expected heterozygosity of 0.03–0.66. Analyses of O. viverrini from 5 localities revealed a high level of genetic diversity and had significant deviation from Hardy–Weinberg equilibrium. Significant heterozygote deficiency as well as heterozygote excess was detected across all localities indicating the possibility of selfing (inbreeding) as a predominant reproductive mode. Significant genetic differentiation ( F ST) was also detected between worms from different localities with varying levels of genetic heterogeneity. We discuss our results in terms of what these novel microsatellite markers reveal about the epidemiology and transmission dynamics of this medically important parasite, both in terms of the current study and their potential for future comprehensive population genetic studies O. viverrini sensu lato in Southeast Asia.

Complex evolution of a highly conserved microsatellite locus in several fish species

The evolutionary dynamics of a highly conserved microsatellite locus (Dla 11) were studied in several fish species. The data indicated that multiple types of compound microsatellites arose through point mutations that were sometimes followed by expansion of the derived motif. Furthermore, extensive length variation was detected among species in the regions immediately flanking the repeat region.

Evidence for Nonindependent Evolution of Adjacent Microsatellites in the Human Genome

Microsatellites are short tandem repeats that evolve predominantly through a stepwise mutation model. Despite intensive study, many aspects of their evolution remain unresolved, particularly the question of how compound microsatellites containing two different motifs evolve. Previous work described profound asymmetries in the probability that any given second motif lies either 3' or 5' of an AC repeat tract. Here we confirm and extend this analysis to examine the length dependence of these asymmetries. We then use the differences in length between homologous human and chimpanzee microsatellites as a surrogate measure of the slippage-based mutation rate to explore factors that influence this process. We find that the dominant predictor of mutation rate is the length of the tract being considered, which is a stronger predictor than the length of the two tracts combined, but other factors also have a significant impact, including the length of the second tract and which of the two tracts lies upstream. We conclude that compound microsatellites rarely arise through random point mutations generating a second motif within a previously pure tract. Instead, our analyses point toward a model in which poorly understood mutation biases, probably affecting both slippage and point mutations and often showing 3'-5' polarity, promote the formation of compound microsatellites. The result is convergent evolution. We suggest that, although their exact nature remains unclear, these biases are likely attributable to structural features, such as the propensity of AC tracts to form Z-DNA.

Heterogeneous Nature and Distribution of Interruptions in Dinucleotides May Indicate the Existence of Biased Substitutions Underlying Microsatellite Evolution

Some aspects of microsatellite evolution, such as the role of base substitutions, are far from being fully understood. To examine the significance of base substitutions underlying the evolution of microsatellites we explored the nature and the distribution of interruptions in dinucleotide repeats from the human genome. The frequencies that we inferred in the repetitive sequences were statistically different from the frequencies observed in other noncoding sequences. Additionally, we detected that the interruptions tended to be towards the ends of the microsatellites and 5'-3' asymmetry. In all the estimates nucleotides forming the same repetitive motif seem to be affected by different base substitution rates in AC and AG. This tendency itself could generate patterning and similarity in flanking sequences and reconcile these phenomena with the high mutation rate found in flanking sequences without invoking convergent evolution. Nevertheless, our data suggest that there is a regional bias in the substitution pattern of microsatellites. The accumulation of random substitutions alone cannot explain the heterogeneity and the asymmetry of interruptions found in this study or the relative frequency of different compound microsatellites in the human genome. Therefore, we cannot rule out the possibility of a mutational bias leading to convergent or parallel evolution in flanking sequences.

Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites

BackgroundCompound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner.ResultsOur in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90%) these motifs differ only by a single mutation (base substitution or indel). We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track.ConclusionOur findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth".

EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

BackgroundMicrosatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database) is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes.DescriptionA user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP). The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided.ConclusionThe database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

SciRoKo: a new tool for whole genome microsatellite search and investigation

SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites. free for use: www.kofler.or.at/Bioinformatics. Supplementary data are available at Bioinformatics online.