The Complete Chloroplast Genome Sequence of Date Palm (<em>Phoenix dactylifera L.</em>)

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.背景 海枣（*Phoenix dactylifera* L.）隶属于棕榈科（Arecaceae），是三大具有重要经济价值的木本棕榈类植物之一，另外两种分别为油棕与椰子树；其果实是中东、北非以及众多热带、亚热带国家的主食之一。本研究基于焦磷酸测序技术，首次报道了海枣叶绿体（chloroplast, cp）基因组的完整序列。 方法与主要结果 我们从全基因组鸟枪测序数据中提取得到369022条叶绿体测序读段，完成了基因组组装，并通过大量PCR验证结合PCR产物测序对组装结果进行了严格校验。海枣叶绿体基因组全长158462 bp，具有典型的四分体结构：由一对反向重复序列（inverted repeats, IRs，27276 bp）分隔的大单拷贝区（large single-copy, LSC，86198 bp）与小单拷贝区（small single-copy, SSC，17712 bp）。与多数被子植物一致，海枣叶绿体基因组包含112个独特基因，以及反向重复区域中的19个重复片段。大单拷贝区/反向重复区（LSC/IR）与小单拷贝区/反向重复区（SSC/IR）的交界区域在进化过程中表现出不同的序列扩张特征。我们在特定叶绿体基因组的种群中鉴定出78个作为种内主要多态性位点的单核苷酸多态性（single nucleotide polymorphism, SNP），其中多数位于具有关键功能的基因内。基于RNA测序数据，我们还发现了18个多顺反子转录单元，以及三个表达偏好性极强的基因：atpF、trnA-UGC与rrn23。 结论 与多数单子叶植物不同，海枣拥有与烟草类似的典型叶绿体基因组，几乎未发生基因组重排、基因丢失或获得事件。高通量测序技术助力鉴定不同栽培品种间叶绿体基因组的种内变异。此外，叶绿体基因的转录组分析为揭示叶绿体转录与翻译的调控机制提供了重要线索。