Transcriptome assemblies for four Argyranthemum taxa (two hybrid species and their parents)

Transcriptome assembly was carried out using Trinity version 2.11 (Grabherr et al., 2013). Read normalisation to k-mer coverage of 30 was carried out prior to assembly. Reads were normalised within species (fru, bro, sun, lem) using Trinity, and for the interspecific assembly ("all") the normalised reads from the four species were combined and normalised again in the same way. Transcripts were assembled with minimum k-mer coverage of 2, increasing the stringency for reads to be assembled together. To account for polymorphism between individuals and species, up to 4 nucleotide differences and a 15 bp gap were allowed when assembling transcripts.