Raw data were first filtered using a previously described pipeline . Briefly, we performed a demultiplexing python script demuladapt (https://github.com/Maillol/demultadapt). Adaptors and low-quality bases were eliminated using cutadapt 1.2.1 . Reads with a mean quality score < 30 were removed using a free perl script https://github.com/SouthGreenPlatform/arcad-hts/blob/master/scripts/arcad_hts_2_Filter_Fastq_On_Mean_Quality.pl . Mapping was performed using default options of BWA aln-sampe V0.7.5a–r405 , and using the D. rotundata transcriptome reference . We validated by modelling that the mapping of genomic DNA reads on a transcriptome reference did not lead to major bias of SNP identification (Additional file 1: Table S1).