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. Correlat...

尽管基因共演化现象已在个体内部以及不同生物类群间被广泛报道，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）因质体基因组演化速率显著升高，成为研究质体-核基因组共演化的理想实验体系。在植物中，质体编码RNA聚合酶（plastid-encoded RNA polymerase，PEP）是一类由质体基因（rpoA、rpoB、rpoC1及rpoC2）与核基因（sig1-6）共同编码亚基的蛋白复合物。本研究利用牻牛儿苗目27个物种的转录组与基因组数据，对编码PEP全酶亚基的基因间的共演化关系开展了系统性评估。研究检测到rpoB/sig1与rpoC2/sig2基因对的非同义替换率（nonsynonymous substitutions，dN）存在显著相关性，而同义替换率（synonymous substitutions，dS）则无此类关联；其余质体/核基因对未观测到该相关性。此外，本研究还鉴定出rpoB/C1/C2与sig1/5/6、rpoC1/C2与sig2，以及rpoB/C2与sig3基因间的dN/dS比值相关性。Correlat...