Microevolution of duplications and deletions and their impact on gene expression in the nematode Pristionchus pacificus

The evolution of diversity across the animal kingdom has been accompanied by tremendous gene loss and gain. While comparative genomics has been fruitful to characterize differences in gene content across highly diverged species, little is known about the microevolution of structural variations that cause these differences in the first place. In order to investigate the genomic impact of structural variations, we made use of genomic and transcriptomic data from the nematode Pristionchus pacificus, which has been established as a satellite model to the well studied nematode model Caenorhabditis elegans for comparative biology. We exploit the fact that P. pacificus is a highly diverse species for which various genomic data including the draft genome of a sister species P. exspectatus is available. Based on resequencing coverage data for two natural isolates we identified large (> 2kb) deletions and duplications relative to the reference strain. By restriction to completely syntenic regions between P. pacificus and P. exspectatus, we were able to polarize the comparison and to assess the impact of structural variations on expression levels. We found that while loss of genes correlates with lack of expression, duplication of genes has virtually no effect on gene expression. Further investigating allelic ratios of sites that segregate between the duplicate copies, we found in the majority of cases only one of the alleles to be expressed, suggesting that one of the copies lacks functionality. Nevertheless, we still find that certain gene classes are strongly depleted in deletions as well as duplications, suggesting an evolutionary constraint acting on synteny. In summary, our results are consistent with a model, where most structural variations are either deleterious or non-functional and provide first insights into the microevolution of structural variations in the P. pacificus genome.