The Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L. cv. ‘Aseel’) Asifullah Khan & Ishtiaq A. Khan & Berthold Heinze & M. Kamran Azim Published online: 23 November 2011 # Springer-Verlag 2011 Abstract Date palm (Phoenix dactylifera L.) is an eco- nomically important and widely cultivated palm of the family Arecaceae. We sequenced the complete date palm chloroplast genome (cpDNA) from Pakistani cv. ‘Aseel’, using a combination of Sanger-based and next-generation sequencing technologies. Being very similar to a sequence from a Saudi Arabian date palm cultivar ‘Khalas’ published recently, the size of the genome was 158,458 bp with a pair of inverted repeat (IR) regions of 27,276 bp that were separated by a large single-copy (LSC) region of 86,195 bp and a small single-copy (SSC) region of 17,711 bp. Genome annotation demonstrated a total of 138 genes, of which 89 were protein coding, 39 were tRNA, and eight were rRNA genes. Comparison of cpDNA sequences of cultivars ‘Aseel’ and ‘Khalas’ showed following intervar- ietal variations in the LSC region; (a) two SNPs in intergenic spacers and one SNP in the rpoc1 gene, (b) polymorphism in two mono-nucleotide simple sequence repeats (SSR), and (c) a 4-bp indel in the accD-psaI intergenic spacer. The SSC region has a polymorphic site in the mono-nucleotide SSR located at position 120,710. We also compared cv. ‘Aseel’ cpDNA sequence with partial P. dactylifera cpDNA sequence entries deposited in Genbank and identified a number of potentially useful polymor- phisms in this species. Analysis of date palm cpDNA sequences revealed a close relationship with Typha latifolia. Occurrence of small numbers of forward and inverted repeats in date palm cpDNA indicated conserved genome arrangement. Keywords Intervarietal polymorphism . Plastid . Next-generation sequencing . Genetic diversity Introduction Date palm (Phoenix dactylifera L.) is an important fruit crop of family Arecaceae mostly grown in the arid regions of Africa, the Middle East, and South Asia (Al-Farsi and Lee 2008). It is one of the oldest known fruit trees cultivated for at least 5,000 years and reported to be originated from southern Iraq or the western Indian subcontinent (Zohary and Hopf 2000). The economic importance of date palm is due to its nutritionally valuable fruit which consists of 72–88% of sugar, minerals (i.e., iron, potassium, calcium, chlorine, copper, magnesium, sulfur, and phosphorus), amino acids, and vitamins (Al-Shahib and Marshall 2003). Moreover, antioxidant and antimutagenic activities of date fruit have also been reported (Vayalil 2002). The date palm tree can grow well in deserts with harsh climatic and soil conditions where the growth of other crops could be relatively difficult. Hence, the date palm offers high nutritive food in such areas (Al-Farsi et al. 2005). In 2006, the world date production was about seven million tonnes (www.faostat.fao.org). Recently, a number of studies have addressed issues of genetic diversity among fruit-bearing plants including date palm (Zhang et al., 2011; He et al., 2011; Tanya et al., A. Khan : I. A. Khan : M. K. Azim (*) International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan e-mail: kamran.azim@iccs.edu M. K. Azim e-mail: mkamranazim@yahoo.co.uk B. Heinze Department of Genetics, Federal Research Centre for Forests, Hauptstraße 7, 1140 Vienna, Austria Plant Mol Biol Rep (2012) 30:666–678 DOI 10.1007/s11105-011-0373-7