title: Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.
abstract: For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested.
authors.affiliation: Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.
authors.forename: Mao-Lun
authors.initials: ML
authors.lastname: Weng
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA.|Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D018628:Gene Dosage; D017343:Genes, Plant; D054627:Genome, Plastid; D055029:Inverted Repeat Sequences / Q000235:genetics*; D031316:Pelargonium / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic
keywords: 
  Pelargonium
  ; genome rearrangement; inverted repeats (IR); nucleotide substitution rate; plastid genome