A Journey from Unravelling the Gene Space to Whole Genome Sequencing of Oil Palm

The road that led to the publication of the oil palm genome sequence was a long and adventurous one. It began with the generation of expressed sequence tags in the late 1990s. This paved the way for the identification of oil palm genes expressed in different tissues and development stages. As technology evolved, MPOB was able to sequence the hypomethylated or gene-rich regions of the genome using the GeneThresher^TM methylation filter technique. About 450,000 sequences from Elaeis guineensis and E. oleifera were generated and this became an important resource for genes and molecular markers, such as microsatellites and single nucleotide polymorphisms (SNP). These markers accelerated the oil palm genetic mapping programme. The next window of opportunity arrived with the introduction of next generation sequencing (NGS). There was initial scepticism on the use of NGS to sequence the oil palm genome, as previous studies had indicated oil palm was an ancient tetraploid with a highly repetitive genome. However, using a combination of NGS paired-end and fragment libraries, as well as BAC end sequencing with the Sanger method, the oil palm genome was sequenced, assembled and annotated.