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1
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0032512051
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The genome sequence of Rickettsia prowazekii and the origin of mitochondria
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The complete genome sequence of the obligate intracellular parasite Rickettsia prowazekii. One of the most remarkable aspects of this genome is its high non-coding content (24%) and the presence of several pseudogenes. The non-coding DNA is speculated to represent remnants of genes that are in their final stages of elimination.
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Andersson S.G.E., Zomorodipour A., Andersson J.O., Sicheritz-Ponten T., Alsmark U.C.M., Podowski R.M., Naslund A.K., Eriksson A-S., Winkler H.H., Kurland C.G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 396:1998;133-140. The complete genome sequence of the obligate intracellular parasite Rickettsia prowazekii. One of the most remarkable aspects of this genome is its high non-coding content (24%) and the presence of several pseudogenes. The non-coding DNA is speculated to represent remnants of genes that are in their final stages of elimination.
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(1998)
Nature
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, pp. 133-140
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Andersson, S.G.E.1
Zomorodipour, A.2
Andersson, J.O.3
Sicheritz-Ponten, T.4
Alsmark, U.C.M.5
Podowski, R.M.6
Naslund, A.K.7
Eriksson, A.-S.8
Winkler, H.H.9
Kurland, C.G.10
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2
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0032561496
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Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
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The complete genome sequence of the obligate intracellular parasite C. trachomatis. The genome lacks many genes for biosynthetic capabilities but encodes an intact glycolytic pathway. In addition, it contains genes coding for a transport system for ATP which enables C. trachomatis to exploit cytosolic ATP as a source of energy.
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Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q.et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 282:1998;754-759. The complete genome sequence of the obligate intracellular parasite C. trachomatis. The genome lacks many genes for biosynthetic capabilities but encodes an intact glycolytic pathway. In addition, it contains genes coding for a transport system for ATP which enables C. trachomatis to exploit cytosolic ATP as a source of energy.
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(1998)
Science
, vol.282
, pp. 754-759
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Stephens, R.S.1
Kalman, S.2
Lammel, C.3
Fan, J.4
Marathe, R.5
Aravind, L.6
Mitchell, W.7
Olinger, L.8
Tatusov, R.L.9
Zhao, Q.10
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3
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0032953228
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Comparative genomes of Chlamydia pneumoniae and C. trachomatis
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The first comparison of two closely related obligate intracellular parasites. The analysis shows that 214 protein coding sequences are uniquely present in the larger genome of C. pneumoniae. The unique genes are dispersed throughout the chromosome.
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Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R.W., Olinger L., Grimwood J., Davis R.W., Stephens R.S. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet. 21:1999;385-389. The first comparison of two closely related obligate intracellular parasites. The analysis shows that 214 protein coding sequences are uniquely present in the larger genome of C. pneumoniae. The unique genes are dispersed throughout the chromosome.
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(1999)
Nat Genet
, vol.21
, pp. 385-389
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Kalman, S.1
Mitchell, W.2
Marathe, R.3
Lammel, C.4
Fan, J.5
Hyman, R.W.6
Olinger, L.7
Grimwood, J.8
Davis, R.W.9
Stephens, R.S.10
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4
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0032934366
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Physical and genetical map of the genome of Buchnera, the primary endosymbiont of the pea aphid Acyrthosiphon pisum
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Charles H., Ishikawa H. Physical and genetical map of the genome of Buchnera, the primary endosymbiont of the pea aphid Acyrthosiphon pisum. J Mol Evol. 48:1999;142-150.
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J Mol Evol
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Charles, H.1
Ishikawa, H.2
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5
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0032127258
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Reductive evolution of resident genomes
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Genome evolution of intracellular bacteria resembles the evolution of organelles in many ways. This review discusses the evolutionary forces acting on genomes that replicate within the cytoplasm of a eukaryotic host cell. The effects of these reductive forces on genome sizes, architectures and nucleotide substitution rates are discussed.
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Andersson S.G.E., Kurland C.G. Reductive evolution of resident genomes. nds Microbiol 6:1998;263-278. Genome evolution of intracellular bacteria resembles the evolution of organelles in many ways. This review discusses the evolutionary forces acting on genomes that replicate within the cytoplasm of a eukaryotic host cell. The effects of these reductive forces on genome sizes, architectures and nucleotide substitution rates are discussed.
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Nds Microbiol
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, pp. 263-278
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Andersson, S.G.E.1
Kurland, C.G.2
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6
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0032993268
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Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis
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This review discusses a comparative analysis of the obligate intracellular parasites R. prowazekii and C. trachomatis. These organisms are not phylogenetically related and it is generally thought that they have adopted to the intracellular environment independently of each other. Both genomes have small genomes sizes, few biosynthetic genes and similar fractions of genes allocated to the different functional categories; however, the identity of genes within the functional categories differ. The most striking difference is that the C. trachomatis genome has a coding content of 89.5%, whereas the R. prowazekii genome has a coding content of only 75.4%.
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Zomorodipour A., Andersson S.G.E. Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis. FEBS Lett. 452:1999;11-15. This review discusses a comparative analysis of the obligate intracellular parasites R. prowazekii and C. trachomatis. These organisms are not phylogenetically related and it is generally thought that they have adopted to the intracellular environment independently of each other. Both genomes have small genomes sizes, few biosynthetic genes and similar fractions of genes allocated to the different functional categories; however, the identity of genes within the functional categories differ. The most striking difference is that the C. trachomatis genome has a coding content of 89.5%, whereas the R. prowazekii genome has a coding content of only 75.4%.
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(1999)
FEBS Lett
, vol.452
, pp. 11-15
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Zomorodipour, A.1
Andersson, S.G.E.2
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7
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0032551756
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A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae
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This is a phylogenetic study based on cytochrome c oxidase I and cytochrome b. The analysis reveals a close phylogenetic relationship between mitochondria and α-proteobacteria in general and between mitochondria and the group of bacteria to which R. prowazekii belongs in particular.
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Sicheritz-Ponten T., Kurland C.G., Andersson S.G.E. A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae. Biochim Biophys Acta. 1365:1998;545-551. This is a phylogenetic study based on cytochrome c oxidase I and cytochrome b. The analysis reveals a close phylogenetic relationship between mitochondria and α-proteobacteria in general and between mitochondria and the group of bacteria to which R. prowazekii belongs in particular.
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Biochim Biophys Acta
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Sicheritz-Ponten, T.1
Kurland, C.G.2
Andersson, S.G.E.3
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8
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0033525788
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Mitochondrial evolution
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An interesting discussion of mitochondrial origin and evolution. Of special interest for the purpose of this review is that all sequenced mitochondrial genomes can be divided into two types: 'the conserved' and 'the derived'. The implication is that there was a first rapid phase of degradation during which a majority of the initial genes were lost, resulting in mitochondrial genomes with similarities to the conserved type of mitochondrial genomes, such as, for example, those found in protists. In some lineages, a second phase of degradation occurred, which resulted in additional gene losses, accelerated mutation rates and non-standard genetic codes. The mammalian mitochondrial genomes are examples of highly derived genomes.
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Gray M.W., Burger G., Lang B.F. Mitochondrial evolution. Science. 283:1999;1476-1481. An interesting discussion of mitochondrial origin and evolution. Of special interest for the purpose of this review is that all sequenced mitochondrial genomes can be divided into two types: 'the conserved' and 'the derived'. The implication is that there was a first rapid phase of degradation during which a majority of the initial genes were lost, resulting in mitochondrial genomes with similarities to the conserved type of mitochondrial genomes, such as, for example, those found in protists. In some lineages, a second phase of degradation occurred, which resulted in additional gene losses, accelerated mutation rates and non-standard genetic codes. The mammalian mitochondrial genomes are examples of highly derived genomes.
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(1999)
Science
, vol.283
, pp. 1476-1481
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Gray, M.W.1
Burger, G.2
Lang, B.F.3
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9
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0032511986
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Rickettsia, typhus and the mitochondrial connection
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A 'News and Views' piece stressing the striking similarities between R. prowazekii and modern mitochondria. The loss of genetic information is most likely a result of convergent reductive evolution, as their common ancestor was almost certainly a free-living microorganism with a larger genome size.
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Gray M.W. Rickettsia, typhus and the mitochondrial connection. Nature. 396:1998;109-110. A 'News and Views' piece stressing the striking similarities between R. prowazekii and modern mitochondria. The loss of genetic information is most likely a result of convergent reductive evolution, as their common ancestor was almost certainly a free-living microorganism with a larger genome size.
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(1998)
Nature
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Gray, M.W.1
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Genome structure and gene content in protist mitochondrial DNAs
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Sankoff, D.6
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Brossard, N.8
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Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant
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dePamphilis C.W., Young N.D., Wolfe A.D. Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation. Proc Natl Acad Sci USA. 94:1997;7367-7372.
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The miniaturized nuclear genome of a eukaryotic endosymbiont contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns
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Gilson P.R., McFadden G.I. The miniaturized nuclear genome of a eukaryotic endosymbiont contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns. Proc Natl Acad Sci USA. 93:1996;7737-7742.
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Gilson P.R., McFadden G.I. Good things in small packages: the tiny genomes of chlorarachniophyte endosymbionts. Bioessays. 19:1997;167-173.
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Genomic rearrangements during evolution of the obligate intracellular parasite Rickettsia prowazekii as inferred from an analysis of 52015 bp nucleotide sequence
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Andersson J.O., Andersson S.G.E. Genomic rearrangements during evolution of the obligate intracellular parasite Rickettsia prowazekii as inferred from an analysis of 52015 bp nucleotide sequence. Microbiology. 143:1997;2783-2795.
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Andersson, J.O.1
Andersson, S.G.E.2
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0032840799
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Genome degradation is an ongoing process in Rickettsia
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The first detailed, comparative analysis of pseudogene sequence evolution in microorganisms. The analysis shows that genes which have been inactivated by frameshift mutations and/or termination codons in the Rickettsia genomes have strongly elevated fixation rates for mutations at sites that cause amino acid replacements, which demonstrates that there is no purifying selection acting on the identified pseudogenes. The analysis also shows that deletions predominate over insertions in these neutral evolving sequences, indicating that an inactivated gene will gradually accumulate substitutions and short deletions until it is no longer recognizable and/or until it is totally eliminated.
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Andersson J.O., Andersson S.G.E. Genome degradation is an ongoing process in Rickettsia. Mol Biol Evol. 16:1999;1178-1191. The first detailed, comparative analysis of pseudogene sequence evolution in microorganisms. The analysis shows that genes which have been inactivated by frameshift mutations and/or termination codons in the Rickettsia genomes have strongly elevated fixation rates for mutations at sites that cause amino acid replacements, which demonstrates that there is no purifying selection acting on the identified pseudogenes. The analysis also shows that deletions predominate over insertions in these neutral evolving sequences, indicating that an inactivated gene will gradually accumulate substitutions and short deletions until it is no longer recognizable and/or until it is totally eliminated.
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Mol Biol Evol
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Andersson, J.O.1
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Uptake and metabolism of S-adenosyl-L-methionine by Leishmania mexicana and Leishmania braziliensis promastigotes
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Amplification of trpEG: Adaptation of Buchnera aphidicola to an endosymbiotic association with aphids
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The endosymbiont (Buchnera sp.) of the aphid Diuraphis noxia contains plasmids consisting of trpEG and tandem repeats of trpEG pseudogenes
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Lai C.Y., Baumann P., Moran N. The endosymbiont (Buchnera sp.) of the aphid Diuraphis noxia contains plasmids consisting of trpEG and tandem repeats of trpEG pseudogenes. Appl Environ Microbiol. 62:1996;332-339.
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Endosymbionts (Buchnera) of the aphid Uroleucon sonchi contain plasmids with trpEG and remnants of trpE pseudogenes
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Baumann L., Clark M.A., Rouhbakhsh D., Baumann P., Moran N.A., Voegtlin D.J. Endosymbionts (Buchnera) of the aphid Uroleucon sonchi contain plasmids with trpEG and remnants of trpE pseudogenes. Curr Microbiol. 35:1997;18-21.
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Baumann, P.4
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25
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0031470826
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Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
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Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R., Lathigra R., White O., Ketchum K.A., Dodson R., Hickey E.K.et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
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Fraser, C.M.1
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Hickey, E.K.10
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26
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0032962345
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Rickettsiae and Chlamydiae: Evidence of horizontal gene transfer and gene exchange
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This analysis of the genomes of the intracellular parasites R. prowazekii and C. trachomatis shows that a total of 16 and 26 proteins, respectively, are most similar to their eukaryotic homologs. The genes coding for these proteins may have been obtained by horisontal transfer. It would be interesting to examine well sampled phylogenetic trees based on these proteins to infer when and from which organisms the putative transfers occured.
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Wolf Y.I., Aravind L., Koonin E.V. Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet. 15:1999;173-175. This analysis of the genomes of the intracellular parasites R. prowazekii and C. trachomatis shows that a total of 16 and 26 proteins, respectively, are most similar to their eukaryotic homologs. The genes coding for these proteins may have been obtained by horisontal transfer. It would be interesting to examine well sampled phylogenetic trees based on these proteins to infer when and from which organisms the putative transfers occured.
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Trends Genet
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Wolf, Y.I.1
Aravind, L.2
Koonin, E.V.3
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27
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0032482924
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Molecular archaeology of the Escherichia coli genome
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2 values of codon usage biases and codon adaptation indices to distinguish between 'native' E. coli genes, and genes which have been introduced recently from another genome with different base composition and/or codon usage patterns. It is concluded that ~18% of the current E. coli chromosome is of foreign origin and has been introduced recently.
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2 values of codon usage biases and codon adaptation indices to distinguish between 'native' E. coli genes, and genes which have been introduced recently from another genome with different base composition and/or codon usage patterns. It is concluded that ~18% of the current E. coli chromosome is of foreign origin and has been introduced recently.
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Proc Natl Acad Sci USA
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Codon usage and base composition in Rickettsia prowazekii
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Evolutionary rates for tuf genes in endosymbionts of aphids
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This paper shows that both synonymous and non-synonymous substitution rates are higher in intracellularly replicating symbionts (Buchnera) than in the free-living microorganisms (E. coli and S. typhimurium). The intrinsic mutation rates for the two lineages were estimated to be very similar, however, suggesting that the fixation rate for synonymous and non-synonymous mutations are significantly higher in the endosymbionts. The results are related to the absence of codon preferences in Buchnera and to the influence of Muller's ratchet on small asexual populations.
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Brynnel E.U., Kurland C.G., Moran N.A., Andersson S.G.E. Evolutionary rates for tuf genes in endosymbionts of aphids. Mol Biol Evol. 15:1998;574-582. This paper shows that both synonymous and non-synonymous substitution rates are higher in intracellularly replicating symbionts (Buchnera) than in the free-living microorganisms (E. coli and S. typhimurium). The intrinsic mutation rates for the two lineages were estimated to be very similar, however, suggesting that the fixation rate for synonymous and non-synonymous mutations are significantly higher in the endosymbionts. The results are related to the absence of codon preferences in Buchnera and to the influence of Muller's ratchet on small asexual populations.
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Mol Biol Evol
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Brynnel, E.U.1
Kurland, C.G.2
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0032515984
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Deleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria
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By examining the free energy of the 16S rRNA genes in a number of bacteria, it has been shown that endosymbiotic bacteria, such as Buchnera have reduced rRNA stabilities compared to their free-living relatives. The results suggest that endosymbiotic bacteria may accumulate slightly deleterious mutations probably as a result of their asexuality and small population sizes.
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Lambert J.D., Moran N.A. Deleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria. Proc Natl Acad Sci USA. 95:1998;4458-4462. By examining the free energy of the 16S rRNA genes in a number of bacteria, it has been shown that endosymbiotic bacteria, such as Buchnera have reduced rRNA stabilities compared to their free-living relatives. The results suggest that endosymbiotic bacteria may accumulate slightly deleterious mutations probably as a result of their asexuality and small population sizes.
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Proc Natl Acad Sci USA
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Evidence for genetic drift in endosymbionts (Buchnera): Analyses of protein-coding genes
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