. "4 Dynamic Evolution of Plant Mitochondrial Genomes: Mobile Genes and Introns and Highly Variable Mutation Rates." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
quent duplications. These most commonly result in small (2–10 members) repeat families whose elements range up to a few hundred base pairs in size, although large duplications and triplications of up to 20 kb are almost always found at least once and sometimes several times within a genome. Angiosperm mtDNAs also grow promiscuously via the relatively frequent capture of sequences from the chloroplast and nucleus (Palmer, 1992; Unseld et al., 1997; Marienfeld et al., 1999). The functional significance of this foreign DNA seems entirely limited to chloroplastderived tRNA genes, which provide many of the tRNAs used in plant mt protein synthesis (Miyata et al., 1998).
Recombination between the small and large repeats scattered throughout angiosperm mtDNAs creates a very dynamic genome structure, both evolutionarily and in real time. Recombination between repeats of about 2 kb and larger is so frequent as to create a dynamic equilibrium in which an individual plant's mtDNA exists as a nearly equimolar mixture of recombinational isomers differing only in the relative orientation of the single copy sequences flanking the rapidly recombining repeats (Palmer, 1990; Mackenzie et al., 1994). Plants such as maize, with many different sets of these large, usually direct “recombination repeats” somehow manage to perpetuate their mt genomes despite their dissolution into a bewildering complexity of subgenomic molecules via repeat-mediated deletion events (Mackenzie et al., 1994; Fauron et al., 1995). Recombination between smaller repeats appears to occur less frequently, although perhaps frequently enough to help maintain a reservoir of low-level, rearranged forms of the genome (termed “ sublimons”) that persist together with the main mt genome. On an evolutionary time-scale, recombination between short dispersed inverted repeats generates large inversions frequently enough to scramble gene order almost completely, even among relatively close members of the same genus (Palmer and Herbon, 1988; Fauron et al., 1995). The combined forces of frequent duplication and inversion have led to the fairly common creation of novel, chimeric genes in plant mitochondria. A number of these chimeric genes lead to cytoplasmic-nuclear incompatibilities manifest as cytoplasmic male sterility (Hanson, 1991; Mackenzie et al., 1994).
The above picture, encapsulated as the title of a 1988 paper (Palmer and Herbon, 1988)—“Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence”—with its corollary that animal mtDNA evolves oppositely in all respects, was largely complete by the late 1980s (Palmer, 1990). This picture was derived from comparison, at both fine-and broad-scale taxonomic levels, of a relatively small number of angiosperms, belonging primarily to but five economically important families [the crucifers (Brassicaceae), the cucurbits (Cucurbitaceae), the legumes (Fabaceae), the grasses (Poaceae), and the nightshades (Solana-