Park Seongjun, Ruhlman Tracey A, Weng Mao-Lun, Hajrah Nahid H, Sabir Jamal S M, Jansen Robert K
Department of Integrative Biology, University of Texas at Austin.
Department of Biology and Microbiology, South Dakota State University.
Genome Biol Evol. 2017 Jun 1;9(6):1766-1780. doi: 10.1093/gbe/evx124.
Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid.
牻牛儿苗科已成为研究质体和线粒体基因组变异的原因及后果的模式系统。在质体基因组（质体基因组）中报道了令人难以置信的结构变异，并且在质体基因组和线粒体基因组（线粒体基因组）的特定谱系和基因功能组中发现了高度加速的进化速率，这些现象与细胞核质不相容性有关。先前的细胞器基因组研究对天竺葵属（该科最大的属，有400多种）的采样有限。本研究报告了17种天竺葵属植物以及其他牻牛儿苗科代表植物的质体基因组和线粒体基因组中的核苷酸替换率和模式。正如在其他被子植物中检测到的那样，在大多数天竺葵属植物中，质体基因组中的替换率比线粒体基因组高3.5倍。然而，在导致布莱斯天竺葵/灰毛天竺葵的分支中，线粒体基因的非同义替换率（dN）和同义替换率（dS）明显高于质体基因，这种模式仅在另一种被子植物中被检测到。此外，两个细胞器基因组的速率加速情况不同，质体基因组的dN增加，而线粒体基因组的dS增加。在暗紫天竺葵/反曲天竺葵分支中，在质体基因组的单拷贝区域检测到经历不对称速率分化的clpP和rpoA基因的重复拷贝。就rpoA而言，导致暗紫天竺葵/反曲天竺葵的分支经历了正选择或纯化选择的放松。最后，乙酰辅酶A羧化酶的进化在牻牛儿苗科中是不寻常的，因为它是第二个在质体中功能上同时存在原核和真核乙酰辅酶A羧化酶的被子植物科。
