Variation and Evolution in Plants and Microorganisms Toward a New Synthesis 50 Years After Stebbins (2000) / Chapter Skim
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4 Dynamic Evolution of Plant Mitochondrial Genomes: Mobile Genes and Introns and Highly Variable Mutation Rates
4 Dynamic Evolution of Plant Mitochondrial Genomes: Mobile Genes and Introns and Highly Variable Mutation Rates
Pages 35-58
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From page 35... ...
These findings mostly arise from a Southern blot survey of gene and intron distribution in 281 diverse angiosperms. These blots reveal numerous losses of mt ribosomal protein genes but, with one exception, only rare loss of respiratory genes.
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From page 36... ...
This extraordinarily invasive mobile element has probably been acquired over 1,000 times separately during angiosperm evolution via a recent wave of cross-species horizontal transfers. Finally, whereas all previously examined angiosperm mtDNAs have low rates of synonymous substitutions, mtDNAs of two distantly related angiosperms have highly accelerated substitution rates.
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From page 37... ...
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~.
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From page 38... ...
We show that rates of gene loss, of accompanying gene transfer to the nucleus, and of intron acquisition by cross-species horizontal transfer can be remarkably high for particular classes of these genetic elements, and that these rates also vary substantially across lineages of flowering plants. As a completely unexpected bonus, these surveys have also led to the discovery of two exceptional groups of plants with vastly elevated rates of synonymous substitutions.
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From page 39... ...
1, while hybridizing strongly to many lanes FIGURE 1. Southern blot survey illustrating three distinct presence/absence patterns of mitochondrial genes and introns.
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From page 40... ...
Our blot surveys will not detect mt pseudogenes unless much or all of the probe region is missing, and thus our survey probably underestimates the number of gene losses. Several ribosomal protein pseudogenes have been reported in angiosperm mt genomes, for example, of rpsl4 and rpsl9
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From page 41... ...
DO MULTIPLE GENE LOSSES REFLECT MULTIPLE GENE TRANSFERS? Assuming that most of the genes lost from the mitochondrion have been transferred to the nucleus, then the many separate losses of each mt ribosomal protein gene and of sdh4 could reflect either an equivalent number of separate transfers, each more or less coincident in time with the loss, or a smaller number of earlier transfers (as few as one for each gene)
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From page 42... ...
, we think that these ribosomal protein genes were not only independently activated but also independently transferred to the nucleus. Considering that rpsl4, rpsil, and rpsl9 have been lost from the mt genomes of many different angiosperm lineages, as revealed by our Southern blot survey, it is possible that each gene has been independently transferred many times, not just twice.
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From page 43... ...
ROLES OF SELECTION AND CHANCE IN MITOCHONDRIAL GENE TRANSFERS DURING ANGIOSPERM EVOLUTION All but the last step (gene loss) in the complicated and evolutionarily unidirectional process by which mt genes move to the nucleus and disap
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From page 44... ...
These prior steps include reverse transcription (which could also occur after either of the next two steps) , exit from the mitochondrion, entry into the nucleus, integration into the nuclear genome, gain of a nuclear promoter and other elements conferring properly
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From page 45... ...
Inactivation of the nuclear copy of a transferred gene results in a failed transfer, but the opportunity for repeated "attempts" at transfer can create a gene transfer ratchet (Doolittle,1998~. Both selection and chance factors may play a role in determining which gene is retained and which gene is inactivated.
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From page 46... ...
Indeed, the only two protein genes contained in all of the many completely sequenced mt genomes encode what are by some criteria (Claros et al., 1995) the two most hydrophobic proteins present in the mitochondrion, cytochrome b and subunit 1 of cytochrome oxidase (Gray et al., 1998; Gray, 1999~.
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From page 47... ...
We are left with a picture of organelle gene transfer as a complex, historically contingent process whose outcome undoubtedly depends on a combination of mechanistically driven factors and chance mutations, together with selective forces. The process seems to be driven by the high rate of physical duplication of organelle genes into the nucleus (which appears to be true for all eukaryotes, regardless of whether functional gene transfer is still occurring)
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From page 48... ...
EXPLOSIVE INVASION OF PLANT MITOCHONDRIA BY A GROUP I INTRON Thus far, we have discussed intracellular horizontal evolution entirely as a means of relocating plant mt genes to the nucleus. As mentioned in the introduction, plant mt genomes are also well known to acquire foreign sequences by intracellular gene transfer, from both the chloroplast and nucleus.
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From page 49... ...
More extensive sampling within the monocot family Araceae showed that 6 of the 14 Araceae sampled contain the intron and that these 6 taxa probably acquired their introns by at least 3 and quite possibly 5 separate horizontal transfers (Cho et al., 1998; Cho and Palmer, 1999~. In addition, unpublished studies from our lab and that of Claude dePamphilis reveal many more cases of independent gain of this promiscuous group I intron.
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From page 50... ...
What does the inevitably complex historical network of horizontal transfers look like; i.e., who is the donor and who is the recipient in each specific instance of intron transfer? Phylogenetic evidence suggests at least one, perhaps initiating long-distance transfer of the intron from a fungus to a flowering plant (Cho et al., 1998~.
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From page 51... ...
These group II introns appear to have been transmitted in a strictly vertical manner, including occasional to frequent losses. HIGHLY ACCELERATED SUBSTITUTION RATES IN TWO LINEAGES OF PLANTS As already emphasized, our wide-scale Southern blot survey for presence or absence of mt genes and introns is predicated entirely on the uncommonly low rates of nucleotide substitutions observed to date in plant mitochondria.
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From page 52... ...
Most critically, in the case of the protein genes, most of the enhanced divergence is confined to synonymous sites. This indicates that the neutral point mutation rate, the rate of occurrence of nucleotide substitutions irrespective of selection, is markedly enhanced in both genera.
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From page 53... ...
POSTSCRIPT Plant mt genomes continue to spring marvelous evolutionary surprises. The discovery that certain angiosperm groups are rapidly moving a large set of mt ribosomal proteins to the nucleus seems remarkable in two contexts: first, that they still have these so "easily transferred" genes left to transfer after a roughly 2-billion-year period of mt existence; second, that animals lost all of these ribosomal protein genes at least 0.6 billion years ago (i.e., before they became animals)
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From page 54... ...
(1995) Maize as a model of higher plant mitochondrial genome plasticity.
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From page 55... ...
(1992) The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.
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From page 56... ...
(1993) Evolution of gene content and gene organization in flowering plant mitochondrial DNA: A general survey and further studies on coxII gene transfer to the nucleus.
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From page 57... ...
(1995) Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coal gene of Peperomia.
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