Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

Dieringer, Daniel; Schlötterer, Christian

doi:10.1101/gr.1416703

Cited by 169 publications

(140 citation statements)

References 41 publications

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“…(Varshney et al 2005;Sharma et al 2007;Grover and Sharma 2011). However, the choice of microsatellite mining criteria and algorithms adopted for the purpose of screening genomic sequences for identifying microsatellites therein offer a lot of diversity (Toth et al 2000;Katti et al 2001;Dieringer and Schlotterer 2003;La Rota et al 2005). Each of the algorithm used in these studies fulfills a certain criteria and accordingly is based on a different principle.…”

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confidence: 99%

Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.

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confidence: 99%

Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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“…There is indication that repeat type and number of repeats have an influence on microsatellite variability (Ellegren, 2000;Dieringer and Schlotterer, 2003). To detect if this is the case in our two sets of data, we The expected homozygosity, (F ) in a sample of the same size and containing the same number of different alleles is calculated per Ewens' expectations using the package PyPop (Lancaster et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Selection on MHC-linked microsatellite loci in sheep populations

et al. 2007

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Microsatellites within the major histocompatibility complex (MHC) region have received increasing attention as proxy measures of the level of polymorphism at the Mhc genes themselves. We assessed the diversity of microsatellite loci within or in close proximity of the Mhc genes in several breeds of domestic sheep (Ovis aries) and the wild Mouflon (Ovis orientalis musimon). This was compared to variation at other microsatellite loci scattered throughout the sheep genome. Significantly higher number of alleles were observed at the MHC microsatellites. The sheep breeds studied fell into high-and low-diversity group. This grouping is not related to the agricultural use of the breeds, whether for milk, meat or wool. It is, however, correlated with the geographic origins of the breeds. Southern breeds are genetically more diverse than northern breeds. The observed heterozygosity was in most cases lower than Hardy-Weinberg expectations. The potential impact of selective breeding by man on this is discussed. Neutrality tests indicated that for most of the breeds, the distribution of alleles at the MHC-linked microsatellites are more even than would be expected if the genes were neutral and sampled from populations under driftmutation equilibrium. Hitchhiking due to tight linkage with alleles at the MHC loci that are under balancing selection is proposed as a possible explanation for this pattern.

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“…Indeed, tracts less than eight nucleotides long seem resistant to slippage, suggesting that there is a critical size above which a homopolymeric tract can be subjected to slippage (Dechering et al 1998). However, computer simulations using analysis of genomic sequences in nine species suggested that short repeats, such as (C) 4 , might have a susceptibility to insertions and deletions 10-15-fold higher than nonrepetitive sequences (Dieringer and Schlotterer 2003). The present study shows that with homopolymeric runs of eight nucleotides or more, there is a tendency toward an increase in the frequency of the variations with the length of the run.…”

Section: Discussionmentioning

confidence: 99%