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1.
Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require
divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3)
only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be
examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using
these methods, we found that mitochondrial genes have 1.7–3.4 times higher synonymous substitution rates than the fastest
nuclear genes or 4.5–9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was
2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred
at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis
that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous
substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two
factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage.
Received: 27 November 1996 / Accepted: 8 May 1997 相似文献
2.
Evidence suggests that the mitochondrial (mt)DNA of anthozoans is evolving at a slower tempo than their nuclear DNA; however,
parallel surveys of nuclear and mitochondrial variations and calibrated rates of both synonymous and nonsynonymous substitutions
across taxa are needed in order to support this scenario. We examined species of the scleractinian coral genus Acropora, including previously unstudied species, for molecular variations in protein-coding genes and noncoding regions of both nuclear
and mt genomes. DNA sequences of a calmodulin ( CaM)-encoding gene region containing three exons, two introns and a 411-bp mt intergenic spacer ( IGS) spanning the cytochrome b ( cytb) and NADH 2 genes, were obtained from 49 Acropora species . The molecular evolutionary rates of coding and noncoding regions in nuclear and mt genomes were compared in conjunction with
published data, including mt cytochrome b, the control region, and nuclear Pax-C introns. Direct sequencing of the mtIGS revealed an average interspecific variation comparable to that seen in published data for mt cytb. The average interspecific variation of the nuclear genome was two to five times greater than that of the mt genome. Based
on the calibration of the closure of Panama Isthmus (3.0 mya) and closure of the Tethy Seaway (12 mya), synonymous substitution
rates ranged from 0.367% to 1.467% Ma −1 for nuclear CaM, which is about 4.8 times faster than those of mt cytb (0.076–0.303% Ma −1). This is similar to the findings in plant genomes that the nuclear genome is evolving at least five times faster than those
of mitochondrial counterparts.
I-Ping Chen and Chung-Yu Tang, co-first author (equal contribution) 相似文献
3.
Background The C↔U substitution types of RNA editing have been observed frequently in organellar genomes of land plants. Although various
attempts have been made to explain why such a seemingly inefficient genetic mechanism would have evolved, no satisfactory
explanation exists in our view. In this study, we examined editing patterns in chloroplast genomes of the hornwort Anthoceros formosae and the fern Adiantum capillus-veneris and in mitochondrial genomes of the angiosperms Arabidopsis thaliana, Beta vulgaris and Oryza sativa, to gain an understanding of the question of how RNA editing originated. 相似文献
4.
Background There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because
orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because
plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying
rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding
regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination
and GC content, that contribute to nucleotide substitution. 相似文献
5.
Previous studies have estimated that, in angiosperms, the synonymous substitution rate of chloroplast genes is three times higher than that of mitochondrial genes and that of nuclear genes is twelve times higher than that of mitochondrial genes. Here we used 12 genes in 27 seed plant species to investigate whether these relative rates of substitutions are common to diverse seed plant groups. We find that the overall relative rate of synonymous substitutions of mitochondrial, chloroplast and nuclear genes of all seed plants is 1:3:10, that these ratios are 1:2:4 in gymnosperms but 1:3:16 in angiosperms and that they go up to 1:3:20 in basal angiosperms. Our results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant groups and that gymnosperms have smaller ratios than angiosperms. 相似文献
6.
Background The mitochondrial DNA (mtDNA) of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific
polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin), by contrast, appears to
evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to
put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that
could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene
from a coral species ( Balanophyllia elegans) known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison
to another coral ( Tubastrea coccinea). 相似文献
7.
Background It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other
land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases
in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation
is across plants. 相似文献
8.
Summary The rate of synonymous nucleotide substitution in nuclear genes of higher plants has been estimated. The rate varies among genes by a factor of up to two, in a manner that is not immediately explicable in terms of base composition or codon usage bias. The average rate, in both monocots and dicots, is about four times higher than that in chloroplast genes. This leads to an estimated absolute silent substitution rate of 6 × 10 –9 substitutions per site per year that falls within the range of average rates (2–8 × 10 –9) seen in different mammalian nuclear genomes. 相似文献
9.
Background Recent phylogenetic studies have revealed that the mitochondrial genome of the angiosperm Silene noctiflora (Caryophyllaceae) has experienced a massive mutation-driven acceleration in substitution rate, placing it among the fastest
evolving eukaryotic genomes ever identified. To date, it appears that other species within Silene have maintained more typical substitution rates, suggesting that the acceleration in S. noctiflora is a recent and isolated evolutionary event. This assessment, however, is based on a very limited sampling of taxa within
this diverse genus. 相似文献
10.
The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein‐coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein‐coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya). 相似文献
11.
Background Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast
DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved
gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown
to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on
gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to
test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged
chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. 相似文献
12.
Key MessageContrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. AbstractThe organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a?>?85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT. 相似文献
13.
Plant cells possess two more genomes besides the central nuclear genome: the mitochondrial genome and the chloroplast genome
(or plastome). Compared to the gigantic nuclear genome, these organelle genomes are tiny and are present in high copy number.
These genomes are less prone to recombination and, therefore, retain signatures of their age to a much better extent than
their nuclear counterparts. Thus, they are valuable phylogenetic tools, giving useful information about the relative age and
relatedness of the organisms possessing them. Unlike animal cells, mitochondrial genomes of plant cells are characterized
by large size, extensive intramolecular recombination and low nucleotide substitution rates and are of limited phylogenetic
utility. Chloroplast genomes, on the other hand, show resemblance to animal mitochondrial genomes in terms of phylogenetic
utility and are more relevant and useful in case of plants. Conservation in gene order, content and lack of recombination
make the plastome an attractive tool for plant phylogenetic studies. Their importance is reflected in the rapid increase in
the availability of complete chloroplast genomes in the public databases. This review aims to summarize the progress in chloroplast
genome research since its inception and tries to encompass all related aspects. Starting with a brief historical account,
it gives a detailed account of the current status of chloroplast genome sequencing and touches upon RNA editing, ycfs, molecular phylogeny, DNA barcoding as well as gene transfer to the nucleus. 相似文献
14.
Background The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants,
and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships
among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns
the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged
before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view.
Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield
misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean
alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. 相似文献
15.
Summary Analysis of the rate of nucleotide substitution at silent sites in Drosophila genes reveals three main points. First, the silent rate varies (by a factor of two) among nuclear genes; it is inversely
related to the degree of codon usage bias, and so selection among synonymous codons appears to constrain the rate of silent
substitution in some genes. Second, mitochondrial genes may have evolved only as fast as nuclear genes with weak codon usage
bias (and two times faster than nuclear genes with high codon usage bias); this is quite different from the situation in mammals
where mitochondrial genes evolve approximately 5–10 times faster than nuclear genes. Third, the absolute rate of substitution
at silent sites in nuclear genes in Drosophila is about three times hihger than the average silent rate in mammals. 相似文献
17.
Background Mitochondrial DNA has been detected in the nuclear genome of eukaryotes as pseudogenes, or Numts. Human and plant genomes harbor a large number of Numts, some of which have high similarity to mitochondrial fragments and thus may have been inadvertently included in population
genetic and phylogenetic studies using mitochondrial DNA. Birds have smaller genomes relative to mammals, and the genome-wide
frequency and distribution of Numts is still unknown. The release of a preliminary version of the chicken ( Gallus gallus) genome by the Genome Sequencing Center at Washington University, St. Louis provided an opportunity to search this first
avian genome for the frequency and characteristics of Numts relative to those in human and plants. 相似文献
18.
We obtained 16 nucleotide sequences (∼1400 bp each) of the first intron of the mitochondrial (mt) gene for NADH subunit 4
(nad4) from 10 species of Brassicaceae. Using these new sequences and five published sequences from GenBank, we constructed
a phylogenetic tree of the Brassicaceae species under study and showed that the rate of nucleotide substitution in the first
intron of nad4 is very low, about 0.16–0.23 × 10 −9 substitution per site per year, which is about half of the silent rate in exons of nad4. The ratios of substitution rates
in this intron, ITS, and IGS are approximately 1:23:73, where ITS is the nuclear intergenic spacer between 18S and 25S rRNA
genes and IGS is the intergenic spacer of 5S rRNA genes. A segment (335 bp) in the first intron of nad4 in Brassicaceae species
that is absent in wheat was considered as a nonfunctional sequence and used to estimate the neutral rate (the rate of mutation)
in mtDNA to be 0.5–0.7 × 10 −9 substitution per site per year, which is about three times higher than the substitution rate in the rest of the first intron
of nad4. We estimated that the dates of divergence are 170–235 million years (Myr) for the monocot–dicot split, 112–156 Myr
for the Brassicaceae–Lettuce split, 14.5–20.4 Myr for the Brassica–Arabidopsis split, and 14.5–20.4 Myr for the Arabidopsis–Arabideae split.
Received: 14 July 1998 / Accepted: 1 October 1998 相似文献
19.
Background The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly
reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine
inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously
impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time,
discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of
plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several
genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface. 相似文献
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