Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.
Genome Biol Evol, 2016/2/17;8(3):622-34.
Zhang J[1], Ruhlman TA[1], Sabir JS[2], Blazier JC[1], Weng ML[1], Park S[1], Jansen RK[3]
Affiliations
PMID: 26893456DOI: 10.1093/gbe/evw033
Impact factor: 4.065
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.
Keywords: nuclear–plastid genome coevolution; nucleotide insertions/deletions; plastid genome rearrangement; substitution rates
MeSH terms
DNA Repair; DNA Replication; Evolution, Molecular; Genome, Plant; Genome, Plastid; Geraniaceae; INDEL Mutation; Phylogeny; Plastids; Recombination, Genetic
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