The attached data files contain two reference transcriptomes of the tomato leafminer, T. absoluta. RNA was extracted from eggs, larvae, pupae and adults of the TA1 strain using the Bioline Isolate II RNA mini kit (Bioline Reagents Ltd., UK), pooled and sent to Eurofins Genomics, Germany, for preparation of a random-primed normalised cDNA library (with an insert size of 150-450 bp) prior to sequencing to ensure the detection of transcripts expressed at even low levels. This was sequenced to high coverage on a single lane of an Illumina HiSeq 2000 using 100bp paired-end sequencing. RNA was extracted from the Spin and SpinSel strains from 3 replicates of 10 larvae from each, as described above, sent to The Genome Analysis CentreTM (TGAC) and multiplexed for sequencing on one lane of an Illumina HiSeq 2000 using 100bp paired-end sequencing. FastQC was used to check the quality of the raw reads obtained (Andrews 2010) prior to de novo assembly using Trinity (Grabherr et al. 2011). Two assemblies were performed: Assembly 1 combined RNAseq data from Spin and SpinSel and assembly 2 combined data from TA1, Spin and SpinSel. Contigs obtained were annotated using Blast2Go (Conesa et al. 2005). The Raw Sequence Data used to assemble these transcriptomes has been deposited in the National Center for Biotechnology Information Sequence Read Archive under the following accession numbers: SRR2846714, SRR2913248, SRR2913250, SRR2913254, SRR2913258, SRR2913261, SRR2913263. References: Grabherr MG, Haas BJ, Yassour M, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644-652. Conesa A, Götz S, García-Gómez JM, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676.