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

TLDR

Date palm is a major woody crop in the Middle East and North Africa, prized for its potential in arid agriculture, but its long generation times and dioecy hinder breeding and genetic studies. The authors aimed to overcome these barriers by generating a draft genome for a Khalas female date palm. They assembled a ~380 Mb draft genome, the first publicly available Arecales resource, and sequenced eight additional cultivars, including females of Deglet Noor and Medjool and their backcrossed males. The draft covers ~90 % of genes and ~60 % of the genome, contains >25,000 gene models, and the comparative analysis uncovered >3.5 million polymorphic sites, >10,000 genic copy‑number variations, a subset distinguishing varieties, and a gender‑linked region supporting an XY inheritance system.

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.