Identification of Transcription Factors from the Hypomethylated Regions of the Oil Palm Genome

Oil palm is an unbranched monoecious plant that belongs to the genus Elaeis. There are two species of oil palm, Elaeis guineensis originating from West Africa and Elaeis oleifera from South and Central America. E. guineensis is widely planted in Malaysia and Indonesia and contributes significantly to the Malaysian and Indonesian economies. With the increasing pressure for sustainability, it is imperative to increase production on the present cultivated land. Due to this, studies on the oil palm genome are important to help improve the understanding of important processes, such as flowering, fruit development and fatty acid biosynthesis and identify genes/markers that could be used to improve productivity. One of the strategies employed is to sequence the hypomethylated regions of the genome, which represents the gene-rich regions. A total of 293,154 sequences were generated from the hypomethylated regions of the E. guineensis genome. An additional 12,443 shot-gun sequences were also generated to access the quality of the libraries constructed. After quality assessment and trimming, the sequences were assembled. Gene models were predicted from the consensus sequences using Maker. These models were compared to the rice and wheat sequences from the Plant Transcriptional Factor Database and validated using InterProScan. A total of 188 oil palm transcription factors from 30 transcription factor gene families were identified. Transcriptional factors, such as Apetala2 (AP2), Leafy (LFY) and MADS-box genes, which are important for flower development, were also identified. These sequences represent an important set of genes to study the different molecular mechanisms in oil palm.