Abstract
Elaeis guineensis
and
E. oleifera
are the two species of oil palm.
E. guineensis
is the most widely cultivated commercial species, and introgression of desirable traits from
E. oleifera
is ongoing. We report an improved
E. guineensis
genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale
E. oleifera
genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697
E. guineensis
and 38,658
E. oleifera
gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.