Data from: Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.

尽管基因共演化现象已在个体内部以及不同生物之间被广泛观测到，但目前极少有研究在系统发育框架下对该现象展开探讨。牻牛儿苗科（Geraniaceae）是研究质体-核基因组共演化（plastid-nuclear genome coevolution）的理想模型系统，因其质体基因组的演化速率显著升高。在植物中，质体编码的RNA聚合酶（plastid-encoded RNA polymerase, PEP）是由质体基因（rpoA、rpoB、rpoC1和rpoC2）与核基因（sig1-6）共同编码亚基所组成的蛋白质复合物。我们利用27种牻牛儿苗目（Geraniales）物种的转录组与基因组数据，系统评估了PEP全酶亚基编码基因之间的共演化关系。我们检测到rpoB/sig1以及rpoC2/sig2组内的非同义替换率（nonsynonymous substitutions, dN）存在显著相关性，但同义替换率（synonymous substitutions, dS）并无此关联；其他质体/核基因对则未出现该现象，同时明确了rpoB/C1/C2与sig1/5/6、rpoC1/C2与sig2、rpoB/C2与sig3各组基因间的dN/dS比值相关性。牻牛儿苗目中相互作用的质体与核序列间的演化速率相关性，可能源于质体-核基因组共演化过程。对共演化氨基酸位点的分析表明，结构介导的共演化并非质体-核共演化的主要驱动因素。本研究检测到SIG与RNAP基因间演化速率的强相关性，这为解释牻牛儿苗科中质体基因组与核基因组不相容性提供了可信的解释。