Linkage map marker sequence assemblies

RAD-tag sequences and paired-end contig assemblies for 11 RAD loci, which were used to develop a linkage map of genetic markers flanking the shell colour (C) and banding presence (B) loci of the Cepaea nemoralis supergene. The sequences were generated by Illumina sequencing of three RAD-Seq libraries comprising both parents and a total 24 F1 offspring from a single cross (C100 x C101) that segregated for shell colour (C) and presence or absence of banding (B). De novo assembly of RAD loci was performed using RADtools 1.2.4 (http://www.RAD-Seq.info). A combination of Unix and Excel commands were then used to identify candidate RAD loci that cosegregate with colour and banding. Paired-end reads were assembled into contigs using VelvetOptimiser version 2.1.7, separately for each of the three RAD libraries. For the RAD markers shown, the corresponding contigs were concatenated and then manually aligned into longer, high-quality contigs. Each sequence is labelled: RAD marker ID – allelic phase with the supergene loci – sequence type – length – coverage. Contigs that could not be aligned are labelled as such.