GBE Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium Seongjun Park1,TraceyA.Ruhlman1,Mao-LunWeng1,2, Nahid H. Hajrah3, Jamal S.M. Sabir3, and Robert K. Jansen1,3,* 1Department of Integrative Biology, University of Texas at Austin 2Department of Biology and Microbiology, South Dakota State University 3Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia *Corresponding author: E-mail:
[email protected]. Accepted: July 3, 2017 Data deposition: All sequences used in this study have been submitted to NCBI Genbank and accession numbers are reported in supplementary tables S10–12, Supplementary Material online. Abstract Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochon- drial 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 signifi- cantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm.