title: Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.
abstract: Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems.
authors.affiliation: Department of Integrative Biology, University of Texas at Austin.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Integrative Biology, University of Texas at Austin.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: The Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.affiliation: Department of Integrative Biology, University of Texas at Austin.
authors.forename: John Chris
authors.initials: JC
authors.lastname: Blazier
authors.affiliation: Department of Integrative Biology, University of Texas at Austin.
authors.forename: Mao-Lun
authors.initials: ML
authors.lastname: Weng
authors.affiliation: Department of Integrative Biology, University of Texas at Austin.
authors.forename: Seongjun
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Integrative Biology, University of Texas at Austin The Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia jansen@austin.utexas.edu.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D054627:Genome, Plastid / Q000235:genetics*; D031314:Geraniaceae / Q000235:genetics*; D054643:INDEL Mutation / Q000235:genetics; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D011995:Recombination, Genetic
keywords: nuclear–plastid genome coevolution; nucleotide insertions/deletions; plastid genome rearrangement; substitution rates