How does sequence variability affect de novo assembly quality?

Date

2013

Authors

Skern-Mauritzen, Rasmus
Malde, Ketil
Besnier, Francois
Nilsen, Frank
Jonassen, Inge
Reinhardt, Richard
Koop, Ben
Dalvin, Sussie
Mæhle, Stig
Kongshaug, Heidi

Journal Title

Journal ISSN

Volume Title

Publisher

Journal of Natural History

Abstract

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.

Description

Keywords

sequencing, assembly, genetic variation, inbreeding

Citation

Skern-Mauritzen, R., Malde, K., Besnier, F., Nilsen, F., Jonassen, I., Reinhardt, B. … Glover, K.A. (2013). How does sequence variability affect de novo assembly quality? Journal of Natural History, 47(5-12), 901-910.