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Figure S1 Histograms representing the length of the contigs and the coverage (number of reads per contig) of the assemblies performed with Newbler and NGen.

Figure S2 Partial assembly of an outlier contig (Contig-00865, unannotated).

Table S1 Parameters used for de novo assembly with programs Newbler (gs de novo Assembler v.2.0.00.20; 454 Life Sciences) and NGen (Seqman NGen™ v1.2, DNA*®) and mapping assembly with gs Reference Mapper (454 Life Sciences).

Table S2 Summary of the gs FLX 454 sequencing run performed on cDNA pools of M and H ecotypes of Littorina saxatilis.

Table S3 Summary of the results of the assemblies performed using Newbler and NGen.

Table S4 Results of the functional annotation performed with Blast2GO.

Table S5 Blastx results for contigs with apparently differential expression between M and H ecotypes for the Newbler assembly.

Table S6 Blastx results for contigs with apparently differential expression between M and H ecotypes for the NGen assembly.

Table S7 Summary of the highly differentiated contigs between H and M ecotypes of L.  saxatilis obtained in the xenobiotics analysis (Blastn search against nr nucleotide database in NCBI).

Table S8 Contigs with outlier loci (P<0.05) that hit BAC clones (E10, E12, A30 and A37) from Littorina saxatilis (see Discussion) after Blastn searches.

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