title: De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera).
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 ∼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.
authors.affiliation: Genomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar.
authors.forename: Eman K
authors.initials: EK
authors.lastname: Al-Dous
authors.forename: Binu
authors.initials: B
authors.lastname: George
authors.forename: Maryam E
authors.initials: ME
authors.lastname: Al-Mahmoud
authors.forename: Moneera Y
authors.initials: MY
authors.lastname: Al-Jaber
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.forename: Yasmeen M
authors.initials: YM
authors.lastname: Salameh
authors.forename: Eman K
authors.initials: EK
authors.lastname: Al-Azwani
authors.forename: Srinivasa
authors.initials: S
authors.lastname: Chaluvadi
authors.forename: Ana C
authors.initials: AC
authors.lastname: Pontaroli
authors.forename: Jeremy
authors.initials: J
authors.lastname: DeBarry
authors.forename: Vincent
authors.initials: V
authors.lastname: Arondel
authors.forename: John
authors.initials: J
authors.lastname: Ohlrogge
authors.forename: Imad J
authors.initials: IJ
authors.lastname: Saie
authors.forename: Khaled M
authors.initials: KM
authors.lastname: Suliman-Elmeer
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Robert R
authors.initials: RR
authors.lastname: Kruegger
authors.forename: Joel A
authors.initials: JA
authors.lastname: Malek
mesh_terms: D000352:Africa, Northern; D000483:Alleles; D028023:Arecaceae / Q000145:classification* / Q000235:genetics*; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D015723:Gene Library; D018745:Genome, Plant; D008877:Middle East; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant