Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

Abstract

The genome sequence of the African oil palm, the main source of oil production, is used to predict at least 34,802 genes, including oil biosynthesis genes; comparison with the draft sequence of the South American oil palm reveals that the two species may have diverged in the New World and that segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. Two papers published in this issue of Nature deal with the genetics of two variants of one of the most important crops in use today — the African oil palm Elaeis guineensis and its South American cousin Elaeis oleifera. Palm oil accounts for almost half the edible oil consumed worldwide and is also a biofuel, although not without controversy, as in many areas palm oil monoculture has replaced valuable natural forest. Analyses of the 1.8-gigabase genome sequence of E. guineensis and draft sequence of E. oleifera provide insights into oil biosynthesis genes and their regulators, and a record of genome evolution. A key event in the domestication and breeding of the oil palm was loss of the thick, coconut-like shell. The second of the two papers identifies mutations the SHELL gene that specify the different fruit forms found in the oil palm and shows that SHELL gene mutations that originated in pre-colonial Africa are responsible for the single gene hybrid vigour and high yields attained by the oil palm. 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 regulators1, 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. guineensis2 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 plantings3, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.