Transcriptome Assembly and Expression Data from Normal and Mantled Oil Palm Fruit

We performed RNA sequencing of fruit from three normal and three mantled (somaclonal variant affecting flower development) oil palm plants using a 454 pyrosequencer. The three normal fruit samples were combined and sequenced, generating 237？748 reads. The three mantled fruit samples were combined and sequenced giving 231？438 reads. The reads were assembled into 13？984 sequences that were clustered into 10？218 genes or gene families. This paper describes the generation of this transcriptome database and includes annotation of these genes from Blast2GO and blast results against the Arabidopsis protein database as well as identification of putative transcription factors. In addition to this, the expression values for each gene sequence of the normal samples are presented. This dataset will be of use to anyone working in oil palm genetics. 1. Introduction Somatic embryogenesis is a desirable way of producing new oil palm plants for oil production [1, 2]. Somatic embryogenesis involves harvesting cells from a donor plant and growth of those cells in media that induces cell division to form a cell mass known as callus which can generate new plants. A somaclonal variant that affects flower development, known as mantled, is observed in oil palm derived from somatic embryogenesis in approximately 5% of plants [3–5] (for recent review see [6]). Currently the only way to identify a mantled oil palm is to wait until it reaches sexual maturity two to four years after planting. Although no data has been published with oil yields, farmers report that mantled fruits have a poor oil yield and no seed is produced. Genomewide hypomethylation has been found in oil palm with the mantled phenotype [7] and no gross genetic abnormalities have been found [8, 9]. The current hypothesis is that the phenotype is caused by epigenetic modification, likely occurring as result of the somatic embryogenesis procedure. The mantled phenotype is expected to change the expression pattern of a number of genes responsible for early flower and fruit development. A promising method that has recently become mainstream is high-throughput RNA sequencing to identify differential expression [10]. In organisms with a published genome, sequence reads are mapped against the genome and gene expression is given as the number of reads that map to each exon [11]. Differential expression in organisms without a genome is done by first generating a de novo assembly and then calculating read counts based on that. This makes RNA sequencing desirable for organisms that do not have an available reference genome,