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

Research output: Contribution to journalArticle

225 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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Genomics
Genes
Genome
Northern Africa
Eastern Africa
Middle East
Polymorphism
Crops
Phoeniceae

ASJC Scopus subject areas

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

Cite this

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). / Aldous, Eman; George, Binu; Al-Mahmoud, Maryam E.; Al-Jaber, Moneera Y.; Wang, Hao; Salameh, Yasmeen M.; Al-Azwani, Eman K.; Chaluvadi, Srinivasa; Pontaroli, Ana C.; Debarry, Jeremy; Arondel, Vincent; Ohlrogge, John; Saie, Imad J.; Suliman-Elmeer, Khaled M.; Bennetzen, Jeffrey L.; Kruegger, Robert R.; Malek, Joel.

In: Nature Biotechnology, Vol. 29, No. 6, 06.2011, p. 521-527.

Research output: Contribution to journalArticle

Aldous, E, George, B, Al-Mahmoud, ME, Al-Jaber, MY, Wang, H, Salameh, YM, Al-Azwani, EK, Chaluvadi, S, Pontaroli, AC, Debarry, J, Arondel, V, Ohlrogge, J, Saie, IJ, Suliman-Elmeer, KM, Bennetzen, JL, Kruegger, RR & Malek, J 2011, 'De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)', Nature Biotechnology, vol. 29, no. 6, pp. 521-527. https://doi.org/10.1038/nbt.1860
Aldous, Eman ; George, Binu ; Al-Mahmoud, Maryam E. ; Al-Jaber, Moneera Y. ; Wang, Hao ; Salameh, Yasmeen M. ; Al-Azwani, Eman K. ; Chaluvadi, Srinivasa ; Pontaroli, Ana C. ; Debarry, Jeremy ; Arondel, Vincent ; Ohlrogge, John ; Saie, Imad J. ; Suliman-Elmeer, Khaled M. ; Bennetzen, Jeffrey L. ; Kruegger, Robert R. ; Malek, Joel. / De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). In: Nature Biotechnology. 2011 ; Vol. 29, No. 6. pp. 521-527.
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