Sequencing the Oil Palm Genome: An Update

Expanding upon previous advances in sequencing the hypomethylated gene space of the oil palm genome, the Malaysian Palm Oil Board (MPOB) has sequenced the E. guineensis and E. oleifera genomes at high coverage by a combination of 454/Roche technology and BAC end sequencing. The genome build is being continually improved by addition of BAC end and whole genome sequencing data. Relative to initial assemblies, the latest E. guineensis build has improved by about 40% measured in terms of N50. A large number of scaffolds from the build were successfully aligned to the 16 linkage groups of the oil palm genetic map, and sequencing of 35 transcriptomes from various tissues enhanced the annotation of the assembly. Additionally, the genome data has been instrumental in the development of genomic platforms such as single nucleotide polymorphism (SNP) arrays and oligoarrays. The genome-wide microarray approach, for example, was successfully applied to detect DNA methylation alterations in clonal palms. This clearly demonstrates that the genome build and tools developed from it provide an opportunity to implement genomics guided breeding and move forward from the phenotype-driven research that had been the focus previously.