De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

Nat Biotechnol. 2011 May 29;29(6):521-7. doi: 10.1038/nbt.1860.


Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5-8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The ∼380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover ∼90% of genes and ∼60% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa, Northern
  • Alleles
  • Arecaceae / classification*
  • Arecaceae / genetics*
  • Chromosome Mapping
  • DNA Copy Number Variations
  • DNA Transposable Elements
  • DNA, Plant / genetics
  • Databases, Genetic
  • Gene Library
  • Genome, Plant*
  • Middle East
  • Pedigree
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA


  • DNA Transposable Elements
  • DNA, Plant