Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes

Huan Gao,Binlun Yan,Baiyao Chen,Fei Yu,Shengli Cai

doi:10.4067/s0716-97602009000300011

Huan Gao, Binlun Yan + Show 3 more

Open Access

https://doi.org/10.4067/s0716-97602009000300011

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Abstract

To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia), rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

Highlights

Microsatellites, called simple sequence repeats (SSRs) or short tandem repeats (STRs), are a class of repetitive DNA sequences widespread in all of eukaryotic genomes (Tautz & Renz, 1984; Aishwarya, 2007) and most prokaryote genomes (Sreenu et al, 2003)
4,960 dinucleotide microsatellite repeats were found in 674 organisms, in which the number of insects (144) is the largest, accounting for 21.36% of total organisms, and the others in decreasing order are plants, fish, birds, amphibians and reptiles, rodentia, mammalia, molluscs, fungi and primates
We found the criterion of extreme value is quiet different among different taxonomic groups, for example, it is ≥11 in the fungi, while it is ≥38 in molluscs

Summary

Introduction

Microsatellites, called simple sequence repeats (SSRs) or short tandem repeats (STRs), are a class of repetitive DNA sequences widespread in all of eukaryotic genomes (Tautz & Renz, 1984; Aishwarya, 2007) and most prokaryote genomes (Sreenu et al, 2003). The typical construction of SSRs consists of 1-6 short motifs repeating many times. It is widely accepted that short protomicrosatellites, which arise by chance in the genome, are expanded by replication slippage, a mutation process which is specific to microsatellite DNA(Schlötterer & Harr, 2000). Slippage mutations occur during DNA replication by displacement of the nascent strand, which subsequently realigns out of register. If DNA synthesis continues on this misplaced DNA molecule, the repeat number of the microsatellite is altered (Tautz & Schlötterer, 1994). SSRs show a high degree of length polymorphism among individuals, and the variability degree in array length can be detected by the number of alleles

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