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United States Department of Agriculture

Agricultural Research Service


Location: National Clonal Germplasm Repository for Citrus

Title: De novo genome sequencing and comparative genomics of the date palm Phoenix dactylifera)

item Al-dous, E
item George, B
item Ai-mahmoud, M
item Al-jaber, M
item Wang, H
item Salameh, Y
item Al-azwani, E
item Chaludavi, S
item Pontaroli, A
item Debarry, J
item Arondel, V
item Ohlrogge, J
item Saie, I
item Bennetzen, J
item Krueger, Robert
item Malek, J

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2011
Publication Date: 5/29/2011
Citation: Al-Dous, E.K., George, B., Ai-Mahmoud, M.E., Al-Jaber, M.Y., Wang, H., Salameh, Y.M., Al-Azwani, E.K., Chaludavi, S., Pontaroli, A.C., Debarry, J., Arondel, V., Ohlrogge, J., Saie, I.J., Bennetzen, J.L., Krueger, R., Malek, J.A. 2011. De novo genome sequencing and comparative genomics of the date palm Phoenix dactylifera). Nature Biotechnology. 29:521-527.

Interpretive Summary: The date palm is native to the Middle East and has been cultivated since ancient times as an important food crop in areas with a climate suitable for its cultivation. It has been difficult in the past to study certain aspects of date palm genetics due to generation time, dioecy, and other factors. To begin to address date palm genomics, 9 date palm genomes were sequenced. OVer 3.5 million polymorphic sites were identified. A small number of these polymorphic sites were useful in distinguishing between different genotypes. A region of the genome linked to sex expression (male and female) was identified.

Technical Abstract: Date Palm has been vital to the Middle East and other arid regions of the world for more than 5000 years. The date palm's ability to withstand extremely harsh conditions, while producing highly nutritious fruit with relatively minimal care, makes it a good candidate for improving arid land agriculture. Challenges such as generation times of approximately 5-8 years and dioecy, separate male and female trees, have hindered genetic studies of the date palm. To provide the foundation for date palm genetic studies, the genome of a 'Khalas' variety female date palm was shotgun sequenced using massively parallel sequencing. A de novo assembly of -380Mbp, spanning mainly gene- rich regions, was generated using only the shotgun reads and over 25,000 gene models were predicted. To help energize date palm biotechnology, 8 additional genomes were sequenced, including those of the economically important Deglet Noor and Medjool variety females together with their backcrossed males. Over 3.5 million polymorphic sites were identified, including >10,000 genic copy number variations. A small subset of polymorphisms capable of distinguishing multiple varieties was discovered. For the first time, a region of the genome linked to gender was identified, and evidence is presented that date palm employs an XY system of gender-inheritance.

Last Modified: 10/20/2017
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