Experiences in Assembling and Annotating the Oil Palm Genome

The oil palm is the most productive oil crop, producing an average of ~4 tonnes of oil per hectare per year in Malaysia. However, the full potential of the crop has not been realized as individual palms in breeding trials have been shown to have yields as high as 14 tonnes of oil per hectare per year. The oil palm has a long breeding cycle (8-12 years), which makes the introduction of new commercial elite planting materials time consuming. This however, can be expedited through the use of genomics-guided breeding, thus leading us to initiate and develop an oil palm genome programme. The oil palm genome, which is approximately 1.8Gb was sequenced, assembled, annotated and published in 2013 using a combination of NGS paired-end and fragment libraries, as well as BAC end sequencing with the Sanger technique. Approximately 44% of the assembled genome was incorporated into pseudochromosomes using genetic maps. Since then, the genome has been significantly improved and updated to allow researchers to use the data more efficiently. This was achieved using new sequencing technologies and by improving the assembly and annotation process. An oil palm genome browser (MYPalmViewer) has also been developed. The browser can be accessed via a link in the Genomsawit portal (http://genomsawit.mpob.gov.my) or directly via http://gbrowse.mpob.gov.my. Here we provide an overview of the developments in MPOB’s Oil Palm Genome Programme and experiences in assembling and annotating the oil palm genome.