The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)

Abstract

BackgroundDate palm (Phoenix dactylifera L.), a member of Arecaceae family, is one of the three major economically important woody palms—the two other palms being oil palm and coconut tree—and its fruit is a staple food among Middle East and North African nations, as well as many other tropical and subtropical regions. Here we report a complete sequence of the data palm chloroplast (cp) genome based on pyrosequencing.Methodology/Principal FindingsAfter extracting 369,022 cp sequencing reads from our whole-genome-shotgun data, we put together an assembly and validated it with intensive PCR-based verification, coupled with PCR product sequencing. The date palm cp genome is 158,462 bp in length and has a typical quadripartite structure of the large (LSC, 86,198 bp) and small single-copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Similar to what has been found among most angiosperms, the date palm cp genome harbors 112 unique genes and 19 duplicated fragments in the IR regions. The junctions between LSC/IRs and SSC/IRs show different features of sequence expansion in evolution. We identified 78 SNPs as major intravarietal polymorphisms within the population of a specific cp genome, most of which were located in genes with vital functions. Based on RNA-sequencing data, we also found 18 polycistronic transcription units and three highly expression-biased genes—atpF, trnA-UGC, and rrn23. ConclusionsUnlike most monocots, date palm has a typical cp genome similar to that of tobacco—with little rearrangement and gene loss or gain. High-throughput sequencing technology facilitates the identification of intravarietal variations in cp genomes among different cultivars. Moreover, transcriptomic analysis of cp genes provides clues for uncovering regulatory mechanisms of transcription and translation in chloroplasts.

Genetic Diversity and the Impact of Geographical Location on the Relationships Between Phoenix dactylifera L. Germplasms Grown in Saudi Arabia

“…Al-Dous et al [22] published the first draft assembly of the sequences of the nuclear date palm genome as a project developed by Weill Cornell Medical College in Qatar (WCMCQ), identifying a region strongly linked to sex determination. Another draft included the date palm chloroplast genome [23]; the project was a joint venture between the Beijing Genomic Centre in China and the King AbdulAziz City for Science and Technology in Riyadh, Saudi Arabia. More recently, the first complete date palm genomic map [24] was constructed based on sequences taken from three males and three females from both Asia and Africa.…”

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

“…Therefore, the genome is widely used to trace the evolutionary history of the plant kingdom. Complete cp DNA sequences have been generated from 104 species of plants, including liverwort (Marchantia polymorpha; Ohyama et al, 1986), black pine (Pinus thunbergii; Wakasugi et al, 1994), rice (Oryza sativa; Hiratsuka et al, 1989), ginseng (Panax schinseng; Kim and Lee, 2004), carrot (Daucus carota; Ruhman et al, 2006), tobacco (Nicotiana tabacum; Shinozaki et al, 1986) and many others (Bausher et al, 2006;Chung et al, 2006;Daniell et al, 2006;Jansen et al, 2006;Jo et al, 2011;Kim et al, 2006;2009;Kuang et al, 2011;Samson et al, 2007;Yang et al, 2010). However, the information currently available on cp genomes is insufficient for elucidating the general evolutionary mechanisms of the genomes or for defining the evolutionary patterns of the plant kingdom.…”

Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives

“…The date industry produced about 7.5 million tons worldwide in 2012 and Saudi Arabia is the third major producer after Egypt and Iran, growing > 400 cultivars 232 . The two most popular cultivars are 'Sukkary' and 'Barhi' 233,234 . However, productivity is neither regular nor easily predictable, particularly so 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 29 since date production is adversely affected by several biotic stress factors [235][236][237] .…”