Year: 2010
Type: article
Abstract: BACKGROUND: Simple sequence repeats (SSRs) are highly variable features of all genomes. Their rapid evolution makes them useful for tracing the evolutionary history of populations and investigating patterns of selection and mutation across genomes. The recently sequenced Daphnia pulex genome provides us with a valuable data set to study the mode and tempo of SSR evolution, without the inherent biases that accompany marker selection. RESULTS: Here we catalogue SSR loci in the Daphnia pulex genome with repeated motif sizes of 1-100 nucleotides with a minimum of 3 perfect repeats. We then used whole genome shotgun reads to determine the average heterozygosity of each SSR type and the relationship that it has to repeat number, motif size, motif sequence, and distribution of SSR loci. We find that SSR heterozygosity is motif specific, and positively correlated with repeat number as well as motif size. For non-repeat unit polymorphisms, we identify a motif-dependent end-nucleotide polymorphism bias that may contribute to the patterns of abundance for specific homopolymers, dimers, and trimers. Our observations confirm the high frequency of multiple unit variation (multistep) at large microsatellite loci, and further show that the occurrence of multiple unit variation is dependent on both repeat number and motif size. Using the Daphnia pulex genetic map, we show a positive correlation between dimer and trimer frequency and recombination. CONCLUSIONS: This genome-wide analysis of SSR variation in Daphnia pulex indicates that several aspects of SSR variation are motif dependent and suggests that a combination of unit length variation and end repeat biased base substitution contribute to the unique spectrum of SSR repeat loci.
Source: BMC Genomics
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,090
Funders: National Science Foundation, U.S. Department of Energy, Eli Lilly and Company, Lilly Endowment, Joint Genome Institute, National Institutes of Health, Office of Science, Biological and Environmental Research, Lawrence Livermore National Laboratory, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory
Awards: G1079818582, G1101028137, G1143651532, G1286236842, G1337544421, G1414775356, G1581387393, G1702950523, G1816284028, G1863003419, G223002938, G2713861829, G2857863752, G3083819904, G3177268909, G3432487278, G365575497, G382641700, G419881185, G42916606, G4501827968, G498139845, G6115782557, G6445123630, G654302390, G7205239661, G7354628648, G7787287669, G797745481, G805243471, G8326222658, G834277795, G8437677540, G969889393
OpenAlex ID: W2162817849