Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae

Abstract

Background: Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago.

Results: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, approximately 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent approximately 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history.

Conclusion: The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and--consistent with the lack of RNA editing--exceptionally high levels of "mutagenic" retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria.

Figure 1

Extreme divergence of mitochondrial genes in Pelargonium hortorum. Shown are ML trees based on synonymous (d_S) sites for protein genes or all sites for rRNA genes. All tree topologies were completely constrained as described in Methods. All d_S trees are drawn to one scale, while all rDNA trees are drawn to a different scale (see bottom right). Abbreviations: Pe, Pelargonium; Pl, Plantago; E, Erodium. (A) Mitochondrial gene trees are based on 1,275 (atp1), 1,119 (cob), 1,413 (cox1), 723 (cox2), 690 (cox3), 805 (LSU rDNA), 1,395 (SSU rDNA), and 198 (nad1) NT. (B) Chloroplast gene trees are based on 1,497 (matK), 2,172 (ndhF), 483 (petD), 1,377 (rbcL), and 417 (rps11) NT. (C) Nuclear gene trees are based on 945 (aco, 1-aminocyclopropane-1-carboxylate oxidase), 1,245 (acs, 1-aminocyclopropane-1-carboxylate synthase), 2,226 (etr, ethylene receptor), and 1,667 (SSU rDNA) NT.

Figure 2

Extensive rate variation in Geraniaceae mitochondrial genes. Shown are ML trees based on synonymous (d_S) or nonsynonymous (d_N) sites for protein genes or all sites for rRNA genes. All tree topologies were completely constrained as described in Methods. To emphasize branch length disparities, taxon names were moved to the right of each tree. Unlabeled branches in the cox1 trees are the same species shown for rbcL. The top three trees are drawn to the same scale, while the bottom three trees are drawn at five times that scale (see scale bars). Abbreviations: Pe, Pelargonium; Pl, Plantago; E, Erodium; G, Geranium. Gene trees are based on 1,413 (cox1), 1,377 (rbcL), 1,471 (mitochondrial SSU rDNA), and 1,667 (nuclear SSU rDNA) NT.

Figure 3

Multigene phylogeny of Geraniaceae and other rosids. Shown is a ML tree based on a 6,226 NT alignment comprising three chloroplast genes (atpB, matK, rbcL) and the nuclear SSU rDNA. Numbers on branches are ML bootstrap values. The tree is rooted using one caryophyllid (Beta) and three asterids. Abbreviations: Pe, Pelargonium; E, Erodium; G, Geranium.

Figure 4

Variable rates of synonymous substitutions in Geraniaceae cox1 genes. Shown is a chronogram based on the topology of Fig. 3. Nodes are labeled A-Z (also see Additional File 1). Shown above each branch are cox1 R_S values (R_S = absolute rate of synonymous substitution per branch) in SSB (sub/site/byr). Abbreviations: Pe, Pelargonium; E, Erodium; G, Geranium. See Additional File 1 for the full set of R_S values taken to two digits after the decimal point, plus full sets of R_N, d_S,d_N,R_N/R_S, and divergence time values.