Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Bioinform Biol Insights
2008 Feb 26;2:157-69. doi: 10.4137/bbi.s561.
Show Gene links
Show Anatomy links
Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.
Xu Z, Gutierrez L, Hitchens M, Scherer S, Sater AK, Wells DE.
???displayArticle.abstract???
The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
Figure 1. Mean tandem repeat number of microsatellite motifs in genomic DNA. Mean repeat numbers were determined for each di-, tri-, and tetranucleotide microsatellite containing a minimum of five perfect tandem repeats. Numbers for the entire genome were estimated from a survey of 444,970,789 base pairs (~25%) of the X. tropicalis genome. Only the four most prevalent motifs for each size class are shown. The AGAT tetranucleotide motif was significantly more common that other tetranucleotide motifs (p < 0.001). Similarly The AT dinucleotide motif was significantly more common that other dinucleotide motifs (p < 0.001). Standard errors are shown.
Figure 2. Relative abundance in genomic and nonredundant DNA of each motif within each of the three microsatellite repeat size classes analyzed. The abundance of each motif within both the genomic sample and the nonredundant sample is plotted against as a percentage of the abundance of the entire size class. AT, ATT, and AGAT were statistically more abundant than other members of their respective size class motif in both genomic and nonredundant samples. Only the most prevalent motifs for each size class are shown. Nonredundant results are shown in black and compared to genomic results are shown in gray.
Figure 3. Mean tandem repeat number in nonredundant DNA for each microsatellite motif. Mean repeat numbers were determined for each di-, tri-, and tetranucleotide contained in our nonredundant microsatellite sample (see methods). Nonredundant results are shown in black, and genomic results are shown in gray. Only the most prevalent motifs for each size class are shown (no GC microsatellites were seen in our nonredundant sample). Standard errors are shown.
Figure 4. Polymorphism rate for repeat length classes of each nonredundant microsatellite motif. Each microsatellite motif was subdivided into seven groups based on the length of their core repeat sequences. The total number of loci analyzed is shown in each length class.
Figure 5. Comparison of polymorphic rates among different microsatellite motifs. Nonredundant microsatellites were tested for polymorphism as described in the methods section. *AAT and ATC show significant higher polymorphism than AAG and AGG (p < 0.001). *AGAT and AAAG are significantly more polymorphic than ACAT and AAAT (p < 0.001).
Amaya,
Xenomics.
2005,
Pubmed
,
Xenbase Bachtrog,
Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome.
1999,
Pubmed Bachtrog,
Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster.
2000,
Pubmed Beckman,
Survey of human and rat microsatellites.
1992,
Pubmed Benson,
Tandem repeats finder: a program to analyze DNA sequences.
1999,
Pubmed Brinkmann,
Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat.
1998,
Pubmed Chakraborty,
Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci.
1997,
Pubmed Cruz,
Distribution and abundance of microsatellites in the genome of bivalves.
2005,
Pubmed Dieringer,
Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species.
2003,
Pubmed Eckert,
Mutational analyses of dinucleotide and tetranucleotide microsatellites in Escherichia coli: influence of sequence on expansion mutagenesis.
2000,
Pubmed Edwards,
The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses.
1998,
Pubmed Ellegren,
Microsatellite mutations in the germline: implications for evolutionary inference.
2000,
Pubmed Ellegren,
Microsatellites: simple sequences with complex evolution.
2004,
Pubmed Estoup,
Characterization of (GT)n and (CT)n microsatellites in two insect species: Apis mellifera and Bombus terrestris.
1993,
Pubmed Goldstein,
Microsatellite variation in North American populations of Drosophila melanogaster.
1995,
Pubmed Hearne,
Microsatellites for linkage analysis of genetic traits.
1992,
Pubmed Jurka,
CENSOR--a program for identification and elimination of repetitive elements from DNA sequences.
1996,
Pubmed Katti,
Differential distribution of simple sequence repeats in eukaryotic genome sequences.
2001,
Pubmed Kayser,
Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs.
2000,
Pubmed La Rota,
Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley.
2005,
Pubmed Lee,
Relative stabilities of dinucleotide and tetranucleotide repeats in cultured mammalian cells.
1999,
Pubmed Levinson,
Slipped-strand mispairing: a major mechanism for DNA sequence evolution.
1987,
Pubmed Li,
Microsatellites within genes: structure, function, and evolution.
2004,
Pubmed Li,
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review.
2002,
Pubmed Metzgar,
Selection against frameshift mutations limits microsatellite expansion in coding DNA.
2000,
Pubmed Moran,
Microsatellite repeats in pig (Sus domestica) and chicken (Gallus domesticus) genomes.
1993,
Pubmed Morgante,
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.
2002,
Pubmed Nadir,
Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.
1996,
Pubmed Neff,
Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats.
2001,
Pubmed Prasad,
Survey and analysis of microsatellites in the silkworm, Bombyx mori: frequency, distribution, mutations, marker potential and their conservation in heterologous species.
2005,
Pubmed Schlötterer,
Slippage synthesis of simple sequence DNA.
1992,
Pubmed Schlötterer,
Evolutionary dynamics of microsatellite DNA.
2000,
Pubmed Schug,
The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster.
1998,
Pubmed Sia,
Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes.
1997,
Pubmed Singh,
Sex- and tissue-specific Bkm(GATA)-binding protein in the germ cells of heterogametic sex.
1994,
Pubmed Subramanian,
Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions.
2003,
Pubmed Subramanian,
MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes.
2002,
Pubmed Talbot,
The tetranucleotide repeat polymorphism D21S1245 demonstrates hypermutability in germline and somatic cells.
1995,
Pubmed Tautz,
Notes on the definition and nomenclature of tandemly repetitive DNA sequences.
1993,
Pubmed Temnykh,
Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential.
2001,
Pubmed Thorén,
Unusually high frequency of (CT)n and (GT)n microsatellite loci in a yellowjacket wasp, Vespula rufa (L.) (Hymenoptera: Vespidae).
1995,
Pubmed Tóth,
Microsatellites in different eukaryotic genomes: survey and analysis.
2000,
Pubmed Weber,
Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms.
1990,
Pubmed Weber,
Mutation of human short tandem repeats.
1993,
Pubmed Zhao,
Visualization of chromosomal domains with boundary element-associated factor BEAF-32.
1995,
Pubmed
