An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Abstract

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.

Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (Phoenix dactylifera)

“…unplaced scaffold (Figure 5A). Using a recently released version of the oil palm genome that places the NW_011550921.1 on chr10 (Ong et al, 2020) we were able to compare our results in more detail. The date palm KDBs showed similarity to the new chr10 between Mb 36 and 51.…”

Heterologous Expression and Characterization of Plant Lipase LIP2 from Elaeis guineensis Jacq. Oil Palm Mesocarp in Escherichia coli

“…A total of 1.535 Gb and 1.2 Gb extended of an assembled sequence and transcriptome of E. guineensis genomic have been covered. There were few lipase-like genes found based on the genes from the prediction method annotation [8,9]. From the genomic domain hit, full ORF for LIP2 gene was analyzed using the ORF finder (https://www.ncbi.nlm.…”

“…Palm oil mostly consists of palmitic acid, however LIP2 did not responsible in degrading the long-chain fatty acids more than C14. There are few lipase genes expressed in oil palm mesocarp [8,9], and LIP2 as one of them can only degrade below carbon chain C14. This might solve some of the contradicting findings between Henderson and Osborne [32] and Ngando et al, [10] on the different biochemical features debate, as it may be that they were focused in characterizing different lipases in oil palm mesocarp.…”

“…During the process of maturation (bruising and abscission), the mesocarp undergoes triglycerides hydrolysis and produces a great amount of free fatty acids. Genome studies have been done before, and more than one lipase-like gene can be found in the mesocarp [8,9]. The lipases from the mesocarp were proven to be serine hydrolases.…”

“…In order to learn more about them, lipase recombinants were constructed and cloned in order to be expressed, purified and characterized. Cloning does more than increase product purity and quality, as clones are also easier to manipulate genetically for better and more stable enzymes with useful biochemical characteristics [9,12]. Lipases extracted from microbial recombinants often have properties that make them more suitable for studies.…”