How does sequence variability affect de novo assembly quality?

Molecular genetic tools have become standard in biological studies of both model and non-model species. This has created a growing need for sequence information, a resource hitherto limited for many species. With new sequencing technologies this is rapidly changing, and whole genome shotgun sequencing has become a realistic goal for many species. However, present sequencing protocols require more DNA than can be extracted from single individuals of many small metazoans, potentially forcing sequencing projects to perform sequencing on samples derived from several individuals. A pertinent question thus arises: can wild samples be used or is inbreeding necessary? In the present study we compare assemblies generated using sequence data from inbred and wild Lepeophtheirus salmonis. The results indicate not only that measures to reduce the genetic variability may significantly improve the final assemblies but also that deeper coverage to some extent can compensate for the detrimental effects of natural sequence variability.