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Oil Palm Genome Sequence Reveals Divergence of Interfertile Species in Old and New Worlds

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Oil Palm Genome Sequence Reveals Divergence of Interfertile Species in Old and New Worlds

Rajinder Singh et al. Nature.

Abstract

Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.

Figures

Fig. 1
Fig. 1. The chromosomes of Oil Palm
E. guineensis has 16 chromosome pairs, ordered by size, which correspond to 16 linkage groups identified by genetic mapping (Supplementary Table 7). Tracks displayed are a, gene density, b, methyl-filtered read density, c, retroelement density, d, SSR repeats, e, low copy number repetitive elements including telomere repeat TTTAGGG (green), 5S rRNA (orange) and pericentromeric repeats (purple), f, regional G+C content (range 0.3–0.45), g, genetically mapped scaffolds from the P5 Build and h, segmental duplications. Densities for telomere repeats are exaggerated for visual clarity.
Fig. 2
Fig. 2. Gene model comparisons
a, Venn Diagram illustrating proportion of shared gene family clusters in oil palm (Eg), banana (Ma), Arabidopsis (At) and date palm (Pd). Number of genes (clusters) compared were At: 27,416 (15,609) Ma: 36,529 (16,874) Pd: 34,804 (16,407) and Eg: 28,882 (16,802). b, GO classifications of oil palm (blue) and date palm (red). c, Ratio of gene number (oil palm:date palm) in each GO classification. Abbreviations: Pt PLP Syn, plastidial phospholipid synthesis; Pt FA Syn, plastidial fatty acid synthesis; OPP, oxidative pentose phosphate; Mal and Pyr met., Malate and Pyruvate Metabolism; Hexoses-P, hexose phosphate pathway; Mt Lipid Syn, mitochondrial lipid synthesis; Deg., degradation; TAG, triacylglycerol; TPs, transporters.
Fig. 3
Fig. 3. Lipid and Carbohydrate metabolism in oil palm fruits
Number of a, lipid synthesis related and b, carbohydrate synthesis related gene transcripts in different tissues. c, Comparison of gene expression levels between kernel and mesocarp tissue prior to and at peak of oil accumulation. Abbreviations: FA Syn, fatty acid synthesis; TAG, triacylglycerol; Pt PLP Syn, plastidial phospholipid synthesis; Glycero, Galacto, Glycero, and Sulfo Lipids; OPP, Oxidative Pentose Phosphate; Mal and Pyr met., Malate and Pyruvate Metabolism.
Fig. 4
Fig. 4. Phylogenetic analysis
A carefully annotated subset of proteins from E. guineensis, E. oleifera and P. dactylifera were included in a matrix of 1,685 gene partitions (858,954 patterns) and 107 taxa. This matrix is extracted from partitions with at least 30 taxa present in a much larger matrix. A maximum likelihood tree of monocotyledonous taxa is shown, along with bootstrap values when less than 100 (Methods Summary). Scale bar indicates the mean number of substitutions per site.

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References

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