Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea

Genome Research

Volumn 11, Issue 6, 2001, Pages 981-993

  Lecompte, Odile ^a   Ripp, Raymond ^a   Puzos Barbe, Valérie ^b   Duprat, Simone ^b   Heilig, Roland ^b   Dietrich, Jacques ^c   Thierry, Jean Claude ^a   Poch, Olivier ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c IFREMER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEOME; TRANSFER RNA;

ADAPTATION; AMINO ACID SUBSTITUTION; ARCHAEBACTERIUM; ARTICLE; BACTERIAL CHROMOSOME; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION FUNCTION; DNA INTEGRATION; ENVIRONMENTAL FACTOR; EVOLUTION; GENE INSERTION; GENE LOCATION; GENE REARRANGEMENT; GENE REPLICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; HYPOTHESIS; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASTICITY; PRIORITY JOURNAL; PYROCOCCUS; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII; THERMOPHILIC BACTERIUM;

ARCHAEAL PROTEINS; CHROMOSOME DELETION; CHROMOSOMES, ARCHAEAL; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; GENES, ARCHAEAL; GENOME, ARCHAEAL; HEAT; MOLECULAR SEQUENCE DATA; PROTEOME; PYROCOCCUS; PYROCOCCUS FURIOSUS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII;

EID: 0034821951     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.GR1653R     Document Type: Article

References (64)

1. Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster
2. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
3. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
4. Insights into the evolutionary process of genome degradation
5. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
6. Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup
7. Deletions at stalled replication forks occur by two different pathways
8. Archaea and the prokaryote-to-eukaryote transition
9. Sulfolobus genome: From genomics to biology
10. The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor
11. DNA repair systems in archaea: Mementos from the last universal common ancestor?
12. Archaeal genomics: Do archaea have a mixed heritage?
13. Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum
14. Pyrococcus abyssi sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent
15. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: Evidence for rolling-circle replication in a hyperthermophile
16. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C
17. Distinguishing homologous from analogous proteins
18. Where is the root of the universal, tree of life?
19. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
20. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough
21. An archaeal genomic signature
22. From complete genomes to measures of substitution rate variability within and between proteins
23. What are archaebacteria: Life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms
24. Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium
25. Genome sequence comparison and scenarios for gene rearrangements: A test case
26. Mycoplasma pneumoniae and Mycoplasma genitalium: A comparison of two closely related bacterial species
27. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium
28. Transfer RNAs and pathogenicity islands
29. Measuring genome evolution
30. Comparative genomes of Chlamydia pneumoniae and C. trachomatis
31. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3
32. Archaebacterial genomes: Eubacterial form and eukaryotic content
33. Prokaryotic genomes: The emerging paradigm of genome-based microbiology
34. Non-orthologous gene displacement
35. The impact of comparative genomics on our understanding of evolution
36. Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
37. Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry?
38. Universal protein families and the functional content of the last universal common ancestor
39. Hyperrecombination in the terminus region of the Escherichia coli chromosome: Possible relation to nucleoid organization
40. Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences
41. Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence
42. Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
43. Testing for equality of evolutionary rates
44. SSV1-encoded site-specific recombination system in Sulfolobus shibatae
45. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon
46. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae
47. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
48. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements
49. Sensitivity of the relative-rate test to taxonomic sampling
50. Phylogenetic invariants for genome rearrangements
51. Rearrangement of the bacterial chromosome: Forbidden inversions
52. Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA
53. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics
54. Genome phylogeny based on gene content
55. Phylogenetic test of the molecular clock and linearized trees
56. A genomic perspective on protein families
57. The genomic tree as revealed from whole proteome comparisons
58. DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
59. Genome plasticity as a paradigm of eubacteria evolution
60. Estimation of primate speciation dates using local molecular clocks