Oilpalm /油棕
Taxonomy: Angiosperms / Monocots / Commelinids /Arecales /Arecaceae/Arecoideae/Cocoseae/Elaeis
Introduction
1. Since palm oil contains more saturated fats than oils made from canola, corn, linseed, soybeans, safflower, and sunflowers, it can withstand extreme deep-frying heat and resists oxidation
2. It contains no trans fat, and its use in food has increased as food-labelling laws have changed to specify trans fat content.
3. Human use of oil palms may date back to about 5,000 years in coastal west Africa.
4. Elaeis guineensis is now extensively cultivated in tropical countries outside Africa, particularly Malaysia and Indonesia which together produce most of the world supply.
5. Palm oil is typically considered the most controversial of the cooking oils - for both health and environmental reasons.
Genomic Version Information
Elaeis guineensis EG5
Genome Overview
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.
Genome Information
| Genome size | 2 Gb |
| Total ungapped length | 1.7 Gb |
| Number of chromosomes | 16 |
| Number of scaffolds | 26 |
| Scaffold N50 | 141.1 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 64,329 |
| Contig N50 | 783.5 kb |
| Contig L50 | 540 |
| GC percent | 39.5 |
| Genome coverage | 48.0x |
Sequencing, Assembly, and Annotation
The assembly of E. guineensis genome P5-build was constructed from sequences from a total of 148linker libraries and 81fragment libraries (Roche/454). Reads were generated from genomic DNA fragment libraries (53.5million reads), BAC pool DNA fragment libraries (3.6million reads), and from a series of genomic (89.1million reads) and BAC (8.6million reads) paired-end linker libraries. In total, 46.8billion bases of raw sequence were generated, representing approximately 26-fold raw sequence coverage of the 1.8-Gb oil palm genome. Sequence data were assembled using the Newbler algorithm28 . The seventh assembly and genome build of E. oleifera (O7-build) was constructed from a total of 127linker libraries and 68fragment libraries. In total, 130million E. oleifera reads, representing approximately 25-fold raw sequence coverage, were generated.
High information content restriction fragment fingerprints were generated for 124,286 BAC clones from the E. guineensis genome with an average size of 150 kb. BAC fingerprints were used to construct a physical map of the reference genome. In addition, BAC ends from this library were sequenced using Sanger sequencing to generate 235,613 paired reads with an average read length of approximately 600 bp. BAC end reads were used to create the shotgun assembly, as well as to locate individual BACs within the assembled genome.
Before assembly, all Roche/454sequence runs were screened for quality based on average read length, linker library efficiency and library redundancy using a custom pipeline based on the SSAHA program29. For linker positive reads, library insert sizes were estimated by aligning both ends to a draft assembly of oil palm, and measuring the intervening sequence in cases in which both ends matched a single draft scaffold. In order to minimize the negative impact of chimaeras in the linker libraries, we removed all identical reads that were due to library redundancy, not independent observations. In addition to the Roche/454 data, a set of 235,613 BAC end reads from the Origen_1 BAC library were included in the P5 assembly, with an average BAC size of 150 kb. These data were assembled using the Newbler algorithm28 on a Dell PowerEdge R910 server with 512 Gb of RAM, and 32 cores running Ubuntu Linux 10.04. The P5 assembly took 15 days and 5 h to complete.
Reference Publication(s)
Singh R et al., "Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds.", Nature, 2013 Aug 15;500(7462):335-9DOI: 10.1038/nature12309