The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)

Abstract

Background: Date 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 findings: After 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.

Conclusions: Unlike 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.

Figure 1. The map of date palm cp genome sequence.

Genes shown outside the outer circle are transcribed clockwise, whereas those shown inside are transcribed counterclockwise. The thick line indicates IRs. The genome coordinate is shown in the inner circle. Genes belonging to different groups are color-coded (Ψ, pseudogene).

Figure 2. A multiple alignment of cemA genes from representative monocot cp genomes.

The start codon is assigned as origin. The possible stop codons in the upstream regions are marked by ellipse. 663-bp less-relevant aligned sequences were omitted.

Figure 3. Expansion of IR into the LSC region.

The dashed lines depict the junction boundaries. The arrowed grey lines indicate the process of IR expansions. a, Amborella and Nicotiana; b, Lemna; c, intermediate; d, Acorus and Dioscorea; e, date palm, typha, and all Poaceaes; f, Phalaenopsis and Oncidium.

Figure 4. Expansion of IR into the SSC region.

The dashed lines depict the junction boundaries. The arrowed grey lines indicate the process of IR expansions. a, Amborella, Nicotiana, typha and two Acoraceae members; b, Phalaenopsis; c, Dioscorea; d, date palm and Arabidopsis; e, intermediate; f, Lemna; g, intermediate; h, most Poaceaes; i, Panicoideae subfamily including Coix, Maize, Saccharum and Sorghum.

Figure 5. Folded stem-loop structures of the new SI from four representative species.

Free energy values (dG) are shown for SI in each species.