Data from: Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae)

Geraniaceae are known for their unusual plastid genomes (plastomes), with the genus Pelargonium being most conspicuous with regard to plastome size and gene organization as judged by the sequenced plastomes of P. x hortorum and P. alternans. However, the hybrid origin of P. x hortorum and the uncertain phylogenetic position of P. alternans obscure the events that led to these extraordinary plastomes. Here, we examine all plastid reconfiguration hotspots for 60 Pelargonium species across all subgenera using a PCR and sequencing approach. Our reconstruction of the rearrangement history revealed four distinct plastome types. The ancestral plastome configuration in the two subgenera Magnipetala and Pelargonium is consistent with that of the P. alternans plastome, whereas that of the subgenus Parvulipetala deviates from this organization by one synapomorphic inversion in the trnNGUU-ndhF region. The plastome of P. x hortorum resembles those of one group of the subgenus Paucisignata, but differs from a second group by another inversion in the psaI-psaJ region. The number of microstructural changes and amount of repetitive DNA are generally elevated in all inverted regions. Nucleotide substitution rates correlate positively with the number of indels in all regions across the different subgenera. We also observed lineage- and species-specific changes in the gene content, including gene duplications and fragmentations. For example, the plastid rbcL-psaI region of Pelargonium contains a highly variable accD-like region. Our results suggest alternative evolutionary paths under possibly changing modes of plastid transmission and indicate the non-functionalization of the plastid accD gene in Pelargonium.牻牛儿苗科(Geraniaceae)植物以其异常的质体基因组(plastome)而闻名，其中天竺葵属(Pelargonium)的质体基因组大小与基因结构最为引人注目，这一点可通过已测序的园艺天竺葵(P. x hortorum)和P. alternans的质体基因组得以证实。然而，园艺天竺葵的杂交起源以及P. alternans不确定的系统发育位置，模糊了导致这些特殊质体基因组形成的演化事件。本研究采用PCR扩增与测序技术，对所有亚属共60个天竺葵属物种的全部质体重排热点区域进行分析。我们对重排历史的重建结果揭示了四种不同的质体基因组类型。大花亚属(Magnipetala)和天竺葵亚属(Pelargonium)的祖先质体基因组结构与P. alternans的质体基因组一致，而小花亚属(Parvulipetala)的质体基因组结构则与该祖先结构存在差异：在trnNGUU-ndhF区域存在一处共源反转(synapomorphic inversion)。园艺天竺葵的质体基因组与少花亚属(Paucisignata)的某一类群的质体基因组相似，但与该亚属另一类群的差异在于psaI-psaJ区域存在另一处反转。所有反转区域的微结构变异数量与重复DNA含量普遍升高。在不同亚属的所有区域中，核苷酸替换速率与插入缺失(indels)数量呈正相关。我们还观察到了谱系与物种特异性的基因含量变异，包括基因复制与片段化事件。例如，天竺葵属的质体rbcL-psaI区域包含一段高度可变的accD样区域。本研究结果揭示了质体传递模式可能发生改变下的多条演化路径，并表明天竺葵属质体accD基因已发生功能丧失。