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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.Especially because date palm orchards, which primarily comprise fruit-bearing female trees, can be rapidly ravished by disease, the ability to quickly replant orchards from seeds or seedlings known to be female would be of great benefit.There are no easily distinguishable sex chromosomes in date palm, despite some cytological evidence that they exist, the identification of DNA sequences or sequence polymorphisms that are gender specific offers a promising alternative to efficiently determine date palm gender.
Post-assembly matching of sequences revealed a sequence redundancy of 53.4× from reads with an average length of 64 bp.We sequenced and assembled the genome of a female tree because, as the fruit-producing trees, female plants are of greater agricultural significance than male trees.The Khalas cultivar we selected to work with is traditionally regarded as the quintessential date variety with very high fruit quality.Scaffolds from the assembly aligned to 60% of the mainly gene-rich total fosmid sequence, giving an indication of the completeness of the draft genome sequence.Analysis of the fosmid sequence not captured in the full genome assembly revealed that the majority of these regions are highly repetitive (Supplementary Notes and Supplementary Table 2).
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This investigation indicates that gene-rich regions were reconstructed more effectively than regions rich in transposable elements, and genes were recovered at much higher frequencies than repeat sequences.