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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 - Bioinform Biol Insights (2008)

Bottom Line: 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.Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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.

No MeSH data available.


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.
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f2-bbi-2008-157: 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.

Mentions: As part of an ongoing effort to identify PCR amplifiable markers for use in developing a genetic map of X. tropicalis, data mining strategies were developed to identify microsatellites embedded in unique sequences suitable for unique genomic localization. To this end, we identified 5,128 non-redundant microsatellites, which were subsequently analyzed elsewhere for polymorphisms (see methods). The distribution and relative abundance of these nonredundant di-, tri-, and tetranucleotide microsatellites is shown in Table 3 and Figure 2. As was seen in the genomic survey, AT, AAT, and AGAT are also the most abundant nonredundant motifs, accounting for 90.30%, 73.52% and 59.48% of di-, tri-, and tetranucleotide motifs respectively (Table 3). Likewise, AC, ATC, and ACAT are the second most abundant motifs in their respective repeat classes. CG repeats, which were found in low numbers in the genomic survey, were absent from our set of nonredundant microsatellites.


Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.

Xu Z, Gutierrez L, Hitchens M, Scherer S, Sater AK, Wells DE - Bioinform Biol Insights (2008)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2735965&req=5

f2-bbi-2008-157: 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.
Mentions: As part of an ongoing effort to identify PCR amplifiable markers for use in developing a genetic map of X. tropicalis, data mining strategies were developed to identify microsatellites embedded in unique sequences suitable for unique genomic localization. To this end, we identified 5,128 non-redundant microsatellites, which were subsequently analyzed elsewhere for polymorphisms (see methods). The distribution and relative abundance of these nonredundant di-, tri-, and tetranucleotide microsatellites is shown in Table 3 and Figure 2. As was seen in the genomic survey, AT, AAT, and AGAT are also the most abundant nonredundant motifs, accounting for 90.30%, 73.52% and 59.48% of di-, tri-, and tetranucleotide motifs respectively (Table 3). Likewise, AC, ATC, and ACAT are the second most abundant motifs in their respective repeat classes. CG repeats, which were found in low numbers in the genomic survey, were absent from our set of nonredundant microsatellites.

Bottom Line: 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.Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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.

No MeSH data available.