Transcriptome Analalysis of the Oil Palm during its Interaction with Thielaviopsis paradoxa

Phenotypic evaluation of oil palm OxG hybrids (Elaeis oleifera X Elaeis guineensis) during their interaction with Thielaviopsis paradoxa, lead to selection of hybrids 485 and 517 for their contrasting response to the pathogen. Transcriptomes of these hybrids during the interaction with T. Paradoxa were sequenced on a  HiSeq2000, producing paired end reads (2x100bp). The experimental setup included one mock sample, i.e., genotype 517 without the interaction with the fungus, one sample of each genotype 485 and 517, inoculated with the pathogen, and the isolated pathogen grown on solid medium. Mock and only-fungus samples were included to disambiguate the source of the sequencing reads for the interaction treatments, i.e., the fungus or the plant. We carried out a de novo assembly of Thielaviopsis paired-end reads using Trinity. Reads from samples that included oil palm transcripts were mapped agains the T. paradoxa transcript assembly. Reads originating from the palm were used to make a new de novo assembly to reconstruct the palm transcriptome. In total 297 million of reads were assigned to palm and 131 million to the fungus. The assembly of the palm reads, also including available ESTs form NCBI, resulted into 115.889. We annotated the putative transcripts using Blast2GO. Several transcripts were assigned to 118 Kegg pathways. Metabolic pathways detected included a-linoeic acid, biosynthesis of ethylene, biosynthesis and cell wall reinforcement, production of reactive oxygen species and production of defense related proteins. Results of differential expression analysis between the tolerant and susceptible genotypes will be presented.