Potato Transcriptome Analysis by RNA-Seq

Transcriptome analyses were performed using RNA-Seq data generated by the PGSC described previously [3] (link). In this data set, transcriptome sequences were generated from 32 DM libraries using RNA-Seq with the Illumina Genome Analyzer II platform (Tables 1 and 2). The 32 DM libraries represent a wide range of developmental tissues/organs as well as abiotic and biotic stress treatments and are described in detail in reference [3] (link) (see Supplementary Material and Table S4). The developmental tissues represent vegetative (leaves, petioles, stolons, tubers sampled twice) and reproductive organs (Floral: carpels, petals, sepals, stamens, whole flowers; Fruit: mesocarp/endocarp, whole immature berries, whole mature berries) from greenhouse-grown plants. Shoots and roots from in vitro-grown plants were also included in the developmental series. Callus (10–11 week old) derived from leaves and stems were used to assess transcription in an undifferentiated tissue. The biotic stress conditions (pooled samples at 24 hr, 36 hr, 72 hr) were induced with Phytophthora infestans inoculum (Pi isolate US8: Pi02-007) and two chemical inducers, acibenzolar-S-methyl (BTH, 100 µg/ml) and DL-β-amino-n-butyric acid (BABA, 2 mg/ml) using detached leaves. Wounded leaves, primary and secondary, were included to mimic herbivory. The abiotic stress conditions (24 hr treatment of in vitro grown whole plants) include heat (35°C), salt (150 mM NaCl) and mannitol (260 µM) treatment. Abscisic acid (ABA, 50 µM), indole-3-acetic acid (IAA, 10 µM), giberellic acid (GA3, 50 µM), and 6 benzylaminopurine (BAP, 10 µM) were used to induce hormone stress responses. Expression levels as previously described in [3] (link) were determined by mapping the RNA-Seq reads to the DM potato reference genome using Tophat [23] (link) and expression levels were determined using Cufflinks [19] . Only representative transcripts, which were chosen by selecting the longest Coding Sequence (CDS) from each gene, were used for the analyses [3] (link). RNA-Seq reads are available in the NCBI Sequence Read Archive under study number SRA029323.