@article{1091484df7b14a60abfa57ee86a187b9,
title = "Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop",
abstract = "Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.",
author = "Hazzouri, {Khaled M.} and Flowers, {Jonathan M.} and Visser, {Hendrik J.} and Khierallah, {Hussam S.M.} and Ulises Rosas and Pham, {Gina M.} and Meyer, {Rachel S.} and Johansen, {Caryn K.} and Fresquez, {Zo{\"e} A.} and Khaled Masmoudi and Nadia Haider and {El Kadri}, Nabila and Youssef Idaghdour and Malek, {Joel A.} and Deborah Thirkhill and Markhand, {Ghulam S.} and Krueger, {Robert R.} and Abdelouahhab Zaid and Purugganan, {Michael D.}",
note = "Funding Information: We thank Marc Arnoux and Brianna Haining for technical assistance in the laboratory, Walter Sanseverino for providing R gene predictions, Sarah Seifi for helping compile the R genes, Florian Maumus for providing REPET predictions of repeats in the date palm genome, Robert J. Williamson for providing the script for heterozgosity calculations, Thomas M. Cahill for the fruit photos, Katherine Dorph for compiling fruit data and Dorian Fuller for illuminating discussions. We also thank Benoit Marchand and Muataz Barwani at New York University Abu Dhabi for assistance with high performance computing, and Nizar Drou for setting up JBrowse. This research was carried out on the High Performance Computing resources at New York University Abu Dhabi. This work was funded in part by grants from the NYU Abu Dhabi Research Institute and the US National Science Foundation Plant Genome Research Program (NSF PGRP), as well as a Human Frontier Science Program Postdoctoral Fellowship to U.R. and an NSF PGRP Postdoctoral Fellowship to R.S.M. J.A.M.{\textquoteright}s contribution to this work was supported by a grant from Qatar Foundation National Research Priorities, NPRPX-014-4-001. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited.",
year = "2015",
month = nov,
day = "9",
doi = "10.1038/ncomms9824",
language = "English",
volume = "6",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
}