The Glanville fritillary metapopulation in the Åland Islands in Finland is a well-known model for studying the ecological, genetic and evolutionary consequences of landscape fragmentation.
We have sequenced the genome of the Glanville fritillary. The Glanville fritillary is the first butterfly species with the ancestral lepidopteran karyotype of 31 and for which both the genome and a high-density linkage map are now available.
The final genome assembly of 393 Mb comprises 1,453 superscaffolds and 4,846 other scaffolds. Superscaffolds (N50=331kb) have linkage map information, and they cover 72% of the genome. The sequencing was based on several outbred individuals using a hybrid sequencing strategy. Extensive validation shows that the assembly is of high quality (more information in Ahola et al. 2014, Supplementary Information).
Several novel methods were developed and used in the genome project. These include a Lep-MAP software for constructing accurate linkage maps using high-density SNP data (Rastas et al. 2013), MIP Scaffolder for genome scaffolding (Salmela et al. 2012), LiSs (Linkage map Superscaffolder) for superscaffolding (unpublished), Coral and HybridSHREC for read error correction (Salmela and Schröder 2011; Salmela 2010), PANNZER for functional annotation (Radivojac et al. 2013) and EPT and SANS for orthology prediction (Ta et al. 2011; Koskinen and Holm 2012).
The genome has been described in:
Ahola V., Lehtonen R., Somervuo P. et al. 2014. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications 5, article number: 4737, doi:10.1038/ncomms5737.
Method for constructing linkage map has been described in:
Rastas P., Paulin L., Hanski I., Lehtonen R., Auvinen P. 2013. Lep-map: Fast and accurate linkage map construction for large snp datasets. Bioinformatics 29, 3128.