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

Eman Aldous, Binu George, Maryam E. Al-Mahmoud, Moneera Y. Al-Jaber, Hao Wang, Yasmeen M. Salameh, Eman K. Al-Azwani, Srinivasa Chaluvadi, Ana C. Pontaroli, Jeremy Debarry, Vincent Arondel, John Ohlrogge, Imad J. Saie, Khaled M. Suliman-Elmeer, Jeffrey L. Bennetzen, Robert R. Kruegger, Joel Malek

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231 Citations (Scopus)

Abstract

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 1/4380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover 1/490% of genes and 1/460% 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.

Original languageEnglish
Pages (from-to)521-527
Number of pages7
JournalNature Biotechnology
Volume29
Issue number6
DOIs
Publication statusPublished - Jun 2011

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ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Aldous, E., George, B., Al-Mahmoud, M. E., Al-Jaber, M. Y., Wang, H., Salameh, Y. M., Al-Azwani, E. K., Chaluvadi, S., Pontaroli, A. C., Debarry, J., Arondel, V., Ohlrogge, J., Saie, I. J., Suliman-Elmeer, K. M., Bennetzen, J. L., Kruegger, R. R., & Malek, J. (2011). De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology, 29(6), 521-527. https://doi.org/10.1038/nbt.1860