Evolution of Chloroplast and Mitochondrial DNA in Plants and Algae

Palmer, Jeffrey D.

doi:10.1007/978-1-4684-4988-4_3

Cited by 164 publications

(100 citation statements)

References 409 publications

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“…Our analysis suggests that cpDNA evolves at only half the rate of plant nDNA, supporting the view that the chloroplast genome evolves slowly (3,5). It is, however, less conservative than plant mtDNA because the synonymous rate in chloroplast genes is 3 times higher (Table 1).…”

Section: Resultssupporting

confidence: 81%

“…Since the plant and animal kingdoms diverged about 1000 million years (Myr) ago, their patterns of evolution might have become very different. In fact, plants differ from animals in the organization oftheir organelle DNA by having a much larger and structurally more variable mitochondrial genome and by having a third (chloroplast) genome (3). So, do the rates of nucleotide substitution differ between animal and plant DNAs?…”

mentioning

confidence: 99%

“…Previous studies based on a few gene sequences or on restriction enzyme mapping have suggested that chloroplast genes have lower rates of nucleotide substitution than mammalian nuclear genes (3,5) and that plant mtDNA evolves slowly in nucleotide sequence, though it undergoes frequent rearrangement (6). Restriction analysis (3,7) has also suggested that the large inverted repeat (IR) sequences in chloroplast DNA (cpDNA) have lower rates of nucleotide substitution than the rest of the chloroplast genome.…”

mentioning

confidence: 99%

“…Restriction analysis (3,7) has also suggested that the large inverted repeat (IR) sequences in chloroplast DNA (cpDNA) have lower rates of nucleotide substitution than the rest of the chloroplast genome. Available DNA sequence data from plants now allow a detailed investigation of the rates of nucleotide substitution in the three plant genomes, reconstruction of the phylogenetic relationships among some higher plants, and comparison of evolutionary rates among lineages.…”

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confidence: 99%

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Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.

Wolfe

Li²,

Sharp³

1987

Proc. Natl. Acad. Sci. U.S.A.

2,014

1,497

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Comparison of plant mitochondrial (mt), chloroplast (cp) and nuclear (n) DNA sequences shows that the silent substitution rate in mtDNA is less than one-third that in cpDNA, which in turn evolves only half as fast as plant nDNA. The slower rate in mtDNA than in cpDNA is probably due to a lower mutation rate. Silent substitution rates in plant and mammalian mtDNAs differ by one or two orders of magnitude, whereas the rates in nDNAs may be similar. In cpDNA, the rate of substitution both at synonymous sites and in noncoding sequences in the inverted repeat is greatly reduced in comparison to single-copy sequences. The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.Our current knowledge of the rates and mechanisms of molecular evolution has been derived largely from comparative studies of genes and proteins of animals (1, 2). Only recently has the study of the molecular biology of plants provided sufficient data to allow the evolution of plant genes to be investigated. Since the plant and animal kingdoms diverged about 1000 million years (Myr) ago, their patterns of evolution might have become very different. In fact, plants differ from animals in the organization oftheir organelle DNA by having a much larger and structurally more variable mitochondrial genome and by having a third (chloroplast) genome (3). So, do the rates of nucleotide substitution differ between animal and plant DNAs? Also, since in mammals mitochondrial DNA (mtDNA) evolves much faster than nuclear DNA (nDNA) (4), do the substitution rates vary greatly among the three plant genomes?Previous studies based on a few gene sequences or on restriction enzyme mapping have suggested that chloroplast genes have lower rates of nucleotide substitution than mammalian nuclear genes (3, 5) and that plant mtDNA evolves slowly in nucleotide sequence, though it undergoes frequent rearrangement (6). Restriction analysis (3, 7) has also suggested that the large inverted repeat (IR) sequences in chloroplast DNA (cpDNA) have lower rates of nucleotide substitution than the rest of the chloroplast genome. Available DNA sequence data from plants now allow a detailed investigation of the rates of nucleotide substitution in the three plant genomes, reconstruction of the phylogenetic relationships among some higher plants, and comparison of evolutionary rates among lineages.MATERIALS AND METHODS DNA sequences were taken from GenBank § and the literature; the sequences of liverwort and tobacco chloroplast genomes (8, 9) were kindly provided on disk by K. Ohyama and M. Sugiura.Numbers of nucleotide substitutions in noncoding sequences were calculated by the two-parameter method of Kimura (1); regions in which the correct alignment was not apparent were excluded from the analysis. Protein-coding genes were analyzed by the method of Li et al. (10) RESULTSRates of Evolution of the Three Plant Genomes. In Table 1 we compare the ...

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Section: Resultssupporting

confidence: 81%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.

Wolfe

Li²,

Sharp³

1987

Proc. Natl. Acad. Sci. U.S.A.

2,014

1,497

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“…During the past decade, geneticists and taxonomists have used restriction endonucleases rather than sequencing to examine variation within and between species in specific segments of DNA (1)(2)(3)(4)(5)(6)(7). Although the indirect assessment of sequence variation obtained with the restriction endonuclease method is known to have many drawbacks, § sequence data have been difficult to obtain.…”

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confidence: 99%

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

Kocher

Thomas

Meyer

et al. 1989

Proc. Natl. Acad. Sci. U.S.A.

4,358

2,533

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With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility ofthese primers offers opportunities for phylogenetic and population research.During the past decade, geneticists and taxonomists have used restriction endonucleases rather than sequencing to examine variation within and between species in specific segments of DNA (1-7). Although the indirect assessment of sequence variation obtained with the restriction endonuclease method is known to have many drawbacks, § sequence data have been difficult to obtain. The construction and screening of clone libraries has been too tedious and have demanded too much expertise for routine use by those geneticists and taxonomists who must analyze many individuals.Dependence on restriction analysis has limited our understanding of the dynamics of DNA sequence evolution. The presence or absence of a restriction site reveals little about the kinds of nucleotide substitutions that have occurred. Thus, although restriction analysis of mtDNA from closely related mammals first showed that these genomes have a higher rate of evolutionary substitution than does nuclear DNA, the demonstration that this acceleration results mainly from an increase in the number of transitions relative to transversions came only from conventional cloning and sequencing (1, 3). Because most studies of animal mtDNA have used restriction analysis, it has been difficult to determine whether a high rate of evolution and a transition bias are characteristic of all animal mtDNAs (8-10). There has been a need for simple methods of sequencing mtDNA to examine the pattern of evolutionary substitution in other animal groups.

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