Tandem-repeat patterns and mutation rates in microsatellites of the nematode model organism Pristionchus pacificus
Autor: | Laure Villate, Iris Dinkelacker, Hanh Witte, Ruxandra I. Molnar, Ralf J. Sommer |
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Rok vydání: | 2012 |
Předmět: |
Mutation rate
Nematoda ved/biology.organism_classification_rank.species Biology Investigations Genome Evolution Molecular Tandem repeat Mutation Rate Genetics Animals Caenorhabditis elegans Molecular Biology Genome size Genetics (clinical) Alleles ved/biology Pristionchus pacificus fungi Mutation Accumulation microsatellite markers tandem repeats mutation accumulation lines Mutation (genetic algorithm) Microsatellite Microsatellite Repeats |
Zdroj: | G3: Genes|Genomes|Genetics |
ISSN: | 2160-1836 |
Popis: | Modern evolutionary biology requires integrative approaches that combine life history, population structure, ecology, and development. The nematode Pristionchus pacificus has been established as a model system in which these aspects can be studied in one organism. P. pacificus has well-developed genetic, genomic, and transgenic tools and its ecologic association with scarab beetles is well described. A recent study provided first mutation rate estimates based on mitochondrial genome sequencing and mutation accumulation line experiments that help resolve rather ancient evolutionary branches. Here, we analyzed the tandem-repeat pattern and studied spontaneous mutation rates for microsatellite markers by using the previously generated mutation accumulation lines. We found that 0.59%–3.83% of the genome is composed of short tandem repeats. We developed 41 microsatellite markers, randomly chosen throughout the genome and analyzed them in 82 mutation accumulation lines after 142 generations. A total of 31 mutations were identified in these lines. There was a strong correlation between allele size and mutation rate in P. pacificus, similar to Caenorhabditis elegans. In contrast to C. elegans, however, there is no evidence for a bias toward multistep mutations. The mutation spectrum of microsatellite loci in P. pacificus shows more insertions than deletions, indicating a tendency toward lengthening, a process that might have contributed to the increase in genome size. The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates. |
Databáze: | OpenAIRE |
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