title: Transcriptome from Fauveliopsis n. sp.
design: Illumina sequencing  High-throughput sequencing was performed using the Illumina platform Genome Analyzer GAII (Illumina, Inc., San Diego, California, USA) and on the HiSeq 2500 at the FAS Center for Systems Biology at Harvard University. The cDNA synthesis, which was performed following methods published elsewhere  (Riesgo, Andrade, et al. 2012) . The Illumina samples were prepared with the NEBNext mRNA Sample Prep kit (New England BioLabs, Ipswich, MA). cDNA was ligated to Illumina adapters, as described earlier  (Riesgo, Andrade, et al. 2012) . Size-selected cDNA fragments of around 300 bp excised from a 2% agarose gel were amplified using Illumina PCR primers for paired-end reads (Illumina, Inc.) and 18 cycles of the PCR program consisting of 98 ºC for 30 s, 98 ºC for 10 s, 65 ºC for 30 s, and 72 ºC for 30 s, followed by an extension step of 5 min at 72 ºC. The concentration of the cDNA libraries was measured with the QubiT® dsDNA High Sensitivity (HS) Assay Kit using the QubiT® Fluorometer (Invitrogen, Carlsbad, California, USA). The quality of the library and size selection were checked using the "HS DNA assay" in a DNA chip for an Agilent Bioanalyzer 2100 (Agilent Technologies, California, USA). For all samples sequenced on Illumina GAII and HiSeq2500 paired-end reads of 150 bp and 100bp read length, respectively, were obtained. Details on the sequencing method and number of raw and processed reads are presented in Table 1.