Total RNA from A. magna K 30097 and A. batizocoi K9484 was extracted from the first expanded leaf of the main axis using the QIAGEN Plant RNeasy kit (QIAGEN) with on-column DNAse treatment. cDNA libraries were constructed using equal amounts of RNA from five individuals of each genotype using the TruSeq v2 library construction kit (Illumina), as described in Leal-Bertioli et al. (2015). To obtain long reads to improve transcriptome assemblies, size-selected libraries were sequenced using MiSEQ v3.0. Adapter and quality trimming was performed using Trim_galore! v0.3.5. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Adapters were trimmed with Cutadapt (http://code.google.com/p/cutadapt/). FastQC (http://galaxy.csdb.cn:8000/tool_runner?tool_id=fastqc) was used to display quality information for cleaned reads. Transcripts were assembled using Trinity (Haas et al. 2013). Assembled transcripts were filtered to include only the longest isoform from each read cluster. The longest isoforms were then aligned to each other by the use of NCBI blastn v2.2.29. Alignments with 100% sequence identity and ≥ 90% sequence length were considered redundant and removed from the final assembly.