Data_Sheet_1_Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes.PDF

The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.

针胞藻纲（Raphidophyceae）是一类兼具初级生产者与捕食者双重功能的重要真核类群，广泛分布于全球海洋与淡水生境。该类群的质体源自真核-真核内共生事件，因此具备极高的进化研究价值。为深入解析针胞藻质体的进化历程，本研究对3种淡水及3种海洋针胞藻物种的质体基因组进行了测序与分析。结合已公开的赤潮异弯藻（Heterosigma akashiwo）质体基因组数据，我们对上述基因组的比较分析揭示了质体基因组结构存在出乎意料的变异。与其他已分析物种的质体基因组不同，裸甲藻（Gonyostomum semen）的质体基因组仅含1个核糖体RNA（rRNA）操纵子，推测这是由于其丢失了多数质体基因组中普遍存在的反向重复（inverted repeat, IR）区域内的基因所致。与之相反，海洋物种日本异刺胞藻（Fibrocapsa japonica）拥有目前已测序针胞藻中最大的IR区域及整体质体基因组，这主要源于其包含4个大型基因间隔区与外源DNA片段。两个质体基因——日本异刺胞藻与赤潮异弯藻中的tyrC基因，以及日本异刺胞藻中的serC基因——似乎通过侧向基因转移（lateral gene transfer, LGT）从硅藻中获得；此外，多个针胞藻的开放阅读框（open reading frame, ORF）经证实与硅藻质粒及质体基因组中的序列具有同源性。日本异刺胞藻psbB基因中的Ⅱ型内含子同样似乎是通过侧向基因转移获得的。本研究通过解析硅藻质体与质粒DNA的侧向基因转移事件，为阐明针胞藻质体基因组的进化历程提供了重要见解。