Data from: How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna

Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within-individual allelic divergence (heterozygosity) however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high-throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by Restriction site Associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re-sequenced the top 18 candidate RAD-loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.Consensus sequencesConsensus sequences with assigned genotype for each individual. 48 text files in total - for each of the four lines, 10 daughter individual files (marked with "d") and files for two mother samples (marked with "m"). _consensus.txt file structure: contig 3'position coverage(sum) haplotype(X-OR-Y) diploid_homozygote(N)-OR-diploid_heterozygote(Y)-OR-haploid_low_coverage(L)-OR-hemizygote(H) consensus_sequenceMarkers_offspring_gntpsFour files - table of marker SNPs for each line and their genotype in each daughter. "_markers_offspring_gtps.txt" file structure: contig locus(3'position) base(SNP) mother.gtp d1 d2 d3 d4 d5 d6 d7 d8 d9 d10 "--"(same_as_mother_genotype) OR "LL"(Low_coverage) OR "NN"(missing genotype) OR different baseSanger_fasta_seqsFasta sequences of re-sequenced RAD-markers (Sanger sequencing). First line (">") denotes the sequenced individual and the primer used. "F" stands for forward and "R" for reverse primerLOH_analysis_pipelinePipeline summary including the code for all step