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.
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.
authors.forename: Khaled M
authors.initials: KM
authors.lastname: Hazzouri
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.|Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Flowers
authors.affiliation: Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates.
authors.forename: Hendrik J
authors.initials: HJ
authors.lastname: Visser
authors.affiliation: Date Palm Research Unit, College of Agriculture, PO Box 47054, University of Baghdad, Baghdad, Iraq.
authors.forename: Hussam S M
authors.initials: HSM
authors.lastname: Khierallah
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Ulises
authors.identifier: http://orcid.org/0000-0001-5088-2679
authors.initials: U
authors.lastname: Rosas
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Gina M
authors.identifier: http://orcid.org/0000-0002-8058-7862
authors.initials: GM
authors.lastname: Pham
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.|Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Rachel S
authors.initials: RS
authors.lastname: Meyer
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Caryn K
authors.initials: CK
authors.lastname: Johansen
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Zoë A
authors.initials: ZA
authors.lastname: Fresquez
authors.affiliation: International Center for Biosaline Agriculture, Academic City, Al Ruwayyah 2, PO Box 14660, Dubai, United Arab Emirates.
authors.forename: Khaled
authors.initials: K
authors.lastname: Masmoudi
authors.affiliation: Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, PO Box 6091, Damascus, Syria.
authors.forename: Nadia
authors.initials: N
authors.lastname: Haider
authors.affiliation: Technical Center of Dates, Ministry of Agriculture, Kebili, Tunisia.
authors.forename: Nabila
authors.initials: N
authors.lastname: El Kadri
authors.affiliation: Division of Science and Mathematics, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.
authors.forename: Youssef
authors.initials: Y
authors.lastname: Idaghdour
authors.affiliation: Genomics Core Laboratory, Weill Cornell Medical College in Qatar, Doha 24144, Qatar.
authors.forename: Joel A
authors.initials: JA
authors.lastname: Malek
authors.affiliation: Arizona State University Date Palm Collection, Arizona State University Tempe, Arizona, Arizona 85281, USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Thirkhill
authors.affiliation: Date Palm Research Institute (DPRI), Shah Abdul Latif University, Khairpur, Sindh, Pakistan.
authors.forename: Ghulam S
authors.initials: GS
authors.lastname: Markhand
authors.affiliation: United States Department of Agriculture, Riverside, California 92507, USA.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Krueger
authors.affiliation: Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates.
authors.forename: Abdelouahhab
authors.initials: A
authors.lastname: Zaid
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.|Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D000352:Africa, Northern; D001208:Asia; D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D008877:Middle East; D008969:Molecular Sequence Data; D065749:Phoeniceae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D014197:Trees / Q000235:genetics
chemical_list: D018744:DNA, Plant