The complete chloroplast genome sequences of three Spondias species reveal close relationship among the species

Abstract This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34–35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content. The inverted repeat regions (IRA and IRB) and the large and small single copies were very similar among the three genomes. The phylogenomic analysis reported similar topologies as that of previous studies, which used partial chloroplast, wherein S. mombin was the first diverging lineage, while S. tuberosa and S. bahiensis were derived, indicating that the phylogenetic analysis using partial or complete genome produces similar results. In summary, (1) we presented the first complete chloroplast genome for the genus Spondias, (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Spondias, and (3) gene order, content, and orientation in Spondias are highly conserved.

摘要 本研究报道了槟榔青属（Spondias）3个物种的完整叶绿体基因组序列。研究采用Illumina测序技术，结合从头组装（de novo）方法与以无患子（Sapindus mukorossi）为参考基因组的参考引导组装策略，对巴西槟榔青（Spondias tuberosa）、巴伊亚槟榔青（Spondias bahiensis）及马槟榔青（Spondias mombin）完成了测序与组装。上述三个物种的叶绿体基因组全长分别为162036 bp、162218 bp和162302 bp。其编码区共包含130个基因，其中包括34~35个转运RNA（tRNA）与4个核糖体RNA（rRNA）。研究结果显示三个叶绿体基因组间存在共线性，基因顺序、基因含量及GC含量均具有高度保守性。三个基因组的反向重复区域（IRA与IRB）以及大单拷贝区、小单拷贝区均极为相似。系统发育基因组学分析结果与此前基于部分叶绿体序列的研究拓扑结构一致：马槟榔青为最先分化的支系，而巴西槟榔青与巴伊亚槟榔青为衍生支系，这表明基于部分或完整叶绿体基因组的系统发育分析可得到相似结果。综上，(1) 本研究首次报道了槟榔青属（Spondias）植物的完整叶绿体基因组序列；(2) 基于完整叶绿体基因组的系统发育分析为槟榔青属植物构建了稳健的系统发育拓扑结构；(3) 槟榔青属植物的基因顺序、基因含量及基因方向均具有高度保守性。