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Bioinform Biol Insights
2008 Feb 26;2:157-69. doi: 10.4137/bbi.s561.
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Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.
Xu Z
,
Gutierrez L
,
Hitchens M
,
Scherer S
,
Sater AK
,
Wells DE
.
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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).
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