Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.
Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.
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DOI：
10.4137/bbi.s561
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发表时间：
2008-02-26
影响因子：
5.8
通讯作者：
Wells DE
中科院分区：
文献类型：
--
作者：
Xu Z;Gutierrez L;Hitchens M;Scherer S;Sater AK;Wells DE
我们的生物信息学分析结果发现，在我们对25%的X染色体的调查中，有超过91，000个二核苷酸、三核苷酸和四核苷酸微卫星。tropicalis基因组，这表明整个基因组中可能有超过360，000个。在X。在热带小蠊基因组中，二核苷酸微卫星（78.7%）的数量远远多于三核苷酸和四核苷酸微卫星。同样，富含AT的重复序列占压倒性优势。在91，304个微卫星中，AT、AAT、AAAT和AATT这4个仅含AT的基序占51，858个，其中AT微卫星是最常见的重复序列，占所有二、三和四核苷酸微卫星的一半以上。这与其他研究的数据形成对比，这些研究表明AC是脊椎动物基因组中最常见的微卫星。此外，我们还确定了5，128个嵌入独特序列的非冗余微卫星的多态性率。有趣的是，这个微卫星亚组被确定为具有比整个基因组微卫星显著更长的重复序列。串联重复序列长度大于30 bp的微卫星位点的多态性显著高于其它位点。两两比较表明，四核苷酸微卫星具有最高的多态性率。此外，AAT和ATC的多态性显著高于其他三核苷酸微卫星，而AGAT和AAAG的多态性显著高于其他四核苷酸微卫星。
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. 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.