uu.seUppsala University Publications
Change search
Refine search result
1 - 34 of 34
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Alsmark, Cecilia
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Comparative Genomics of Obligate and Facultative Intracellular Parasites2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The α-proteobacteria Rickettsia prowazekii and Bartonella henselae are the causative agents of epidemic typhus and cat scratch disease respectively. Whereas R. prowazekii is an obligate intracellular parasite, B. henselae can live and proliferate both outside and inside the eukaryotic host cell. Besides the obvious medical interest to identify the complete gene set of two human pathogens, their genome sequences are also important for the study of evolutionary processes. Both R. prowazekii and B. henselae have small genomes, but their last common ancestor of these two bacteria was most likely a free-living organism with a substantially larger genome.

    The aim of this thesis is to compare the complete genomes of R. prowazekii and B. henselae and to decipher the evolutionary processes leading to the adaptation to an intracellular lifestyle. The working hypothesis was that the facultative intracellular B. henselae is an intermediate between a free living bacteria and the obligate R. prowazekii, which is corroborated. B. henselae has a broader biosynthetic repertoire than R. prowazekii, including the presence of genes for glycolysis and de novo biosynthesis of purines and pyrimidines. However, both bacteria have reduced gene sets for biosynthesis of amino acids and cofactors compared to free-living bacteria.

    Comparisons of gene order in bacteria reveal that several operons are well conserved between distantly related species. The genome sequences of R. prowazekii and B. henselae show that many of the operons that are usually conserved, are broken and rearranged in these species. One of the mechanisms of reductive evolution include intra-chromosomal recombination between repeated loci. This process expels one of the repeats and cause rearrangements in the gene order of the flanking regions. While the R. prowazekii genome almost completely lack repeated sequences, the B. henselae genome is rich in repeats. These repeats are, however, most often located within regions associated with pathogenicity islands. The higher number of scrambled operons, and the lower number of repeats, in R. prowazekii compared to B. henselae imply that the reductive process has gone further in the former species.

  • 2.
    Amiri, H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Alsmark, U. C. M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Andersson, S. G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Proliferation and deterioration of Rickettsia palindromic elements2002In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 19, no 8, p. 1234-1243Article in journal (Refereed)
    Abstract [en]

    It has been suggested that Rickettsia Palindromic Elements (RPEs) have evolved as selfish DNA that mediate protein sequence evolution by being targeted to genes that code for RNA and proteins. Here, we have examined the phylogenetic depth of two RPEs that are located close to the genes encoding elongation factors Tu (tuf) and G (fus) in Rickettsia. An exceptional organization of the elongation factor genes was found in all 11 species examined, with complete or partial RPEs identified downstream of the tuf gene (RPE-tuf) in six species and of the fus gene (RPE-fus) in 10 species. A phylogenetic reconstruction shows that both RPE-tuf and RPE-fus have evolved in a manner that is consistent with the expected species divergence. The analysis provides evidence for independent loss of RPE-tuf in several species, possibly mediated by short repetitive sequences flanking the site of excision. The remaining RPE-tuf sequences evolve as neutral sequences in different stages of deterioration. Likewise, highly fragmented remnants of the RPE-fus sequence were identified in two species. This suggests that genome-specific differences in the content of RPEs are the result of recent loss rather than recent proliferation.

  • 3.
    Amiri, H.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Andersson, S. G. E.
    Rickettsia: The highly rearranged cousin of mitochondria2001In: Recent Res. Dev. Microbiol., Vol. 5, p. 321-329Article in journal (Refereed)
  • 4.
    Amiri, H.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Davids, W.
    Andersson, S. G. E.
    Evolution of intergenic DNA in RickettsiaManuscript (Other academic)
  • 5.
    Amiri, H.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Karlberg, O.
    Andersson, S. G. E.
    In the phylogenetic footsteps of ATP- ADP translocasesManuscript (Other academic)
  • 6.
    Amiri, Haleh
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Patterns and Processes of Molecular Evolution in Rickettsia2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Species of the genus Rickettsia are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses.

    This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions and duplications in a variety of Rickettsia species. The results show that early intrachromosomal recombination events mediated by duplicated genes and short repeats have resulted in deletions as well as rearrangements. For example, an exceptional organization of the elongation factor genes was found in all species examined, suggesting that this rearrangement event occurred at the early stage of the evolution of Rickettsia. Likewise, it was found that a repetitive element, the so-called Rickettsia Palindromic Element (RPE) flourished prior to species divergence in Rickettsia. Finally, a phylogenetic analysis shows that the duplication events that gave rise to the five genes encoding ATP/ADP transporters occurred long before the divergence of the two major groups of Rickettsia. Taken together, this suggests that Rickettsia have been intracellular parasites for an extensive period of time.

    A detailed analysis of the patterns of nucleotide changes in genes and intergenic regions among the different species provides evidence for a gradual accumulation of short deletions. This suggests that different distributions of genes and repeated sequences in modern Rickettsia species reflect species-specific differences in rates of deterioration rather than variation in rates of intra-genomic sequence proliferation.

    List of papers
    1. A chimeric disposition of the elongation factor genes in Rickettsia prowazekii
    Open this publication in new window or tab >>A chimeric disposition of the elongation factor genes in Rickettsia prowazekii
    Show others...
    1996 In: J. Bacteriol., Vol. 178, p. 6192-6199Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-89688 (URN)
    Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved
    2. Proliferation and deterioration of Rickettsia palindromic elements
    Open this publication in new window or tab >>Proliferation and deterioration of Rickettsia palindromic elements
    2002 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 19, no 8, p. 1234-1243Article in journal (Refereed) Published
    Abstract [en]

    It has been suggested that Rickettsia Palindromic Elements (RPEs) have evolved as selfish DNA that mediate protein sequence evolution by being targeted to genes that code for RNA and proteins. Here, we have examined the phylogenetic depth of two RPEs that are located close to the genes encoding elongation factors Tu (tuf) and G (fus) in Rickettsia. An exceptional organization of the elongation factor genes was found in all 11 species examined, with complete or partial RPEs identified downstream of the tuf gene (RPE-tuf) in six species and of the fus gene (RPE-fus) in 10 species. A phylogenetic reconstruction shows that both RPE-tuf and RPE-fus have evolved in a manner that is consistent with the expected species divergence. The analysis provides evidence for independent loss of RPE-tuf in several species, possibly mediated by short repetitive sequences flanking the site of excision. The remaining RPE-tuf sequences evolve as neutral sequences in different stages of deterioration. Likewise, highly fragmented remnants of the RPE-fus sequence were identified in two species. This suggests that genome-specific differences in the content of RPEs are the result of recent loss rather than recent proliferation.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-89689 (URN)12140235 (PubMedID)
    Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
    3. In the phylogenetic footsteps of ATP- ADP translocases
    Open this publication in new window or tab >>In the phylogenetic footsteps of ATP- ADP translocases
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89690 (URN)
    Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2010-01-13Bibliographically approved
    4. Evolution of intergenic DNA in Rickettsia
    Open this publication in new window or tab >>Evolution of intergenic DNA in Rickettsia
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89691 (URN)
    Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2010-01-13Bibliographically approved
    5. Loss of gene function: Clues from expressed gene fragments in Rickettsia
    Open this publication in new window or tab >>Loss of gene function: Clues from expressed gene fragments in Rickettsia
    2002 (English)In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 18, no 7, p. 331-334Article in journal (Refereed) Published
    Abstract [en]

    Many obligate intracellular pathogens have small genomes with high fractions of pseudogenes. A recent analysis of gene expression patterns in Rickettsia conorii shows that short open reading frames inside deteriorating genes are occasionally transcribed into RNA. Here, we show that substitution frequencies at nonsynonymous sites are similar for expressed and unexpressed parts of the fragmented genes. We conclude that the observed expression is a temporary stage in the gene degradation process, suggesting that the expressed gene fragments are not functional.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-89692 (URN)10.1016/S0168-9525(02)02685-9 (DOI)
    Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
    6. Genome deterioration: Loss of repeated sequences and accumulation of junk DNA
    Open this publication in new window or tab >>Genome deterioration: Loss of repeated sequences and accumulation of junk DNA
    2002 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 115, no 1, p. 1-12Article in journal (Refereed) Published
    Abstract [en]

    A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-89693 (URN)12188042 (PubMedID)
    Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
    7. Rickettsia: The highly rearranged cousin of mitochondria
    Open this publication in new window or tab >>Rickettsia: The highly rearranged cousin of mitochondria
    2001 In: Recent Res. Dev. Microbiol., Vol. 5, p. 321-329Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-89694 (URN)
    Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved
  • 7.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Brishammar, Sture
    Biology and partial sequencing of an endophytic Fusarium oxysporum and plant defense complexManuscript (Other academic)
  • 8.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Levenfors, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Brishammar, Sture
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    A rapid molecular method for differentiating two special forms (lycopersici and radicis-lycopersici) of Fusarium oxysporum2004In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 108, no 7, p. 787-794Article in journal (Refereed)
    Abstract [en]

    Two pathogenic special forms (f. sp.) of the Fusarium oxysporum species complex f. sp. lycopersici (Fol) and f. sp. radicis-lycopersici (Forl) are morphologically indistinguishable. Although they are pathogenic to the same host genus Lycopersicon (tomato), and infect the same tomato cultivar, they form distinct diseases; Fol causes wilt and Forl causes crown rot and root rot. These two special forms apparently exist as genetically isolated populations, based on vegetative compatibility and molecular variation at the DNA level. In seeking efficient diagnostic tools for differentiating Fol and Forl isolates, we examined three techniques: isozyme analysis, mitochondrial DNA (mtDNA) RFLP by HaeIII-digestion of total genomic DNA, and an osmotic method using high performance liquid chromatography (HPLC) to detect fungal pigments. The isolates were collected from geographically widespread locations. Distinct HPLC-profile differences were found between an endophytic non-pathogenic isolate and the other pathogenic isolates. However, the direct mtDNA RFLP technique proved to be an efficient diagnostic tool for routine differentiation of Fol and Forl isolates.

  • 9.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Johansson, Petra Maria
    Brishammar, Sture
    Gerhardson, Berndt
    Pseudomonas sp. strain MF30 suppresses Fusarium wilt of tomato in vivo2001In: Phytopathologia Mediterranea, ISSN 0031-9465, Vol. 40, no 3, p. 234-239Article in journal (Refereed)
  • 10.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Johnson, Paul
    Brishammar, Sture
    Quintanilla, Pablo
    Systemic resistance to Fusarium wilt in tomato induced by Phytophthora cryptogea2001In: Journal of Phytopathology, ISSN 0931-1785, Vol. 149, no 7-8, p. 373-380Article in journal (Refereed)
  • 11.
    Berg, Otto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Jain, Mahendra
    Interfacial Enzyme Kinetics2002Book (Other academic)
    Abstract [en]

    This guide concentrates on the chemical and physical foundation of enzyme catalysis, the key area for the deeper understanding of biocatalytic processes. It also includes examples for proteins and nucleic acids, two central areas of biochemical and bio-organic research.

  • 12.
    Björkman, J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Nagaev, I
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Berg, O G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Hughes, Diarmaid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andersson, Dan I
    Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance2000In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 287, no 5457, p. 1479-1482Article in journal (Refereed)
    Abstract [en]

    Most types of antibiotic resistance impose a biological cost on bacterial fitness. These costs can be compensated, usually without loss of resistance, by second-site mutations during the evolution of the resistant bacteria in an experimental host or in a laboratory medium. Different fitness-compensating mutations were selected depending on whether the bacteria evolved through serial passage in mice or in a laboratory medium. This difference in mutation spectra was caused by either a growth condition-specific formation or selection of the compensated mutants. These results suggest that bacterial evolution to reduce the costs of antibiotic resistance can take different trajectories within and outside a host.

  • 13.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Loss of Mitochondrial tRNA Genes Correlates with Loss of Genes for Aminoacyl-tRNA SynthetasesManuscript (Other academic)
    Abstract [en]

    Most mitochondrial genomes encode their own tRNAs, whereas the mitochondrial aminoacyl-tRNA synthetases (aaRS) are encoded by the nuclear genome. It has been suggested that the loss of mitochondrial tRNA genes from the mitocchondrial genome correlates with the sequence similarity between bacterial and eukaryotic aaRSs, in that aaRSs that are similar across the two domains can easily shift between charging mitochondrial and cytosolic tRNAs (Schneider 2001). However, recent work has shown that mitochondrial and cytosolic aaRSs have complex evolutionary histories and are not always of bacterial and eukaryotic origin, respectively (Brindefalk et al. 2007). We repeated the analysis performed by Schneider using all available mitochondrial genomes as of December 2006 and found that the loss of mitochondrial tRNA genes correlates with replacements of the genes for the corresponding aaRS. Our observations provide new insights into the co-evolution of mitochondrial tRNAs and their charging enzymes.

  • 14.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Ettema, Thijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Tholleson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.Manuscript (Other academic)
    Abstract [en]

     

    Background

    According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans.

     

    Principal Findings

    Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation.

     

    Conclusions/Significance

    Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.

     

  • 15.
    Davids, Wagied
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Amiri, Haleh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Loss of gene function: Clues from expressed gene fragments in Rickettsia2002In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 18, no 7, p. 331-334Article in journal (Refereed)
    Abstract [en]

    Many obligate intracellular pathogens have small genomes with high fractions of pseudogenes. A recent analysis of gene expression patterns in Rickettsia conorii shows that short open reading frames inside deteriorating genes are occasionally transcribed into RNA. Here, we show that substitution frequencies at nonsynonymous sites are similar for expressed and unexpressed parts of the fragmented genes. We conclude that the observed expression is a temporary stage in the gene degradation process, suggesting that the expressed gene fragments are not functional.

  • 16.
    Frank, A. Carolin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Amiri, Haleh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Genome deterioration: Loss of repeated sequences and accumulation of junk DNA2002In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 115, no 1, p. 1-12Article in journal (Refereed)
    Abstract [en]

    A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.

  • 17. Garibaldi, A.
    et al.
    Bertetti, D.
    Vinnere, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Gullino, M.L.
    Presence of Colletotrichum acutatum causing leaf spot on Azalea japonica in Italy2004In: Plant Disease, ISSN 0191-2917, E-ISSN 1943-7692, Vol. 88, no 5, p. 572-Article in journal (Refereed)
    Abstract [en]

    Rhododendron cultivation has a long history in northern Italy where a wide selection of varieties and hybrids are grown. In the fall of 2002, a previously unknown disease was observed on Azalea japonica cv. Palestrina in several commercial farms in the Province of Verbania. Leaves showed irregular necrotic areas that were 1 mm in diameter. Lesions were dark brown to black and were surrounded by a chlorotic halo. Eventually, lesions coalesced, forming large irregular spots. Heavily infected leaves fell prematurely, resulting in severe defoliation. On the infected leaves, acervuli were present from which cylindrical tapered conidia measuring 4.8 to 7.2 × 11.0 to 22.8 μm at one end were released. Fifty conidia per isolate were measured. Fungus identified as Colletotrichum acutatum was consistently recovered from infected leaves, disinfested in 1% NaOCl for 1 min, and plated on potato dextrose agar amended with 100 mg/l of streptomycin sulfate. Pathogenicity of three fungal isolates was confirmed by inoculating healthy A. japonica (cvs. Palestrina and Snow) plants grown in plastic pots (18-cm diameter, 3 liters). Plants (five per treatment) were sprayed with a conidial suspension (1 × 106 conidia per ml) of the three isolates of C. acutatum. Noninoculated plants served as a control. Inoculated and control plants were covered with plastic bags to maintain high relative humidity conditions. All plants were maintained in growth chambers at 20 ± 1°C (12 h per day of fluorescent light). Six days after the artificial inoculation, plants developed typical symptoms on the leaves. C. acutatum was consistently reisolated from infected plants. The pathogenicity test was carried out twice. Sequencing of the internal transcribed spacer region of the rDNA and a portion of the β-tubulin gene were performed, and the obtained sequences were compared with those available in GenBank. Identification of the fungus as C. acutatum, therefore was confirmed. To our knowledge, this is the first report of the presence of C. acutatum on A. japonica in Italy. Although observed presently only in a few nurseries, the disease has the potential to spread, becoming more relevant in an area where rhododendron cultivation is economically important. Anthracnose on rhododendron has already been described in several countries (1,2).

  • 18.
    Hooper, Sean
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Dynamics of Microbial Genome Evolution2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The success of microbial life on Earth can be attributed not only to environmental factors, but also to the surprising hardiness, adaptability and flexibility of the microbes themselves. They are able to quickly adapt to new niches or circumstances through gene evolution and also by sheer strength of numbers, where statistics favor otherwise rare events.

    An integral part of adaptation is the plasticity of the genome; losing and acquiring genes depending on whether they are needed or not. Genomes can also be the birthplace of new gene functions, by duplicating and modifying existing genes. Genes can also be acquired from outside, transcending species boundaries. In this work, the focus is set primarily on duplication, deletion and import (lateral transfer) of genes – three factors contributing to the versatility and success of microbial life throughout the biosphere.

    We have developed a compositional method of identifying genes that have been imported into a genome, and the rate of import/deletion turnover has been appreciated in a number of organisms. Furthermore, we propose a model of genome evolution by duplication, where through the principle of gene amplification, novel gene functions are discovered within genes with weak- or secondary protein functions. Subsequently, the novel function is maintained by selection and eventually optimized. Finally, we discuss a possible synergic link between lateral transfer and duplicative processes in gene innovation.

    List of papers
    1. Gradients in nucleotide and codon usage along Escherichia coli genes
    Open this publication in new window or tab >>Gradients in nucleotide and codon usage along Escherichia coli genes
    2000 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 28, no 18, p. 3517-3523Article in journal (Refereed) Published
    Abstract [en]

    The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-90104 (URN)10.1093/nar/28.18.3517 (DOI)110745 (PubMedID)
    Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
    2. Detection of genes with atypical nucleotide sequence in microbial genomes
    Open this publication in new window or tab >>Detection of genes with atypical nucleotide sequence in microbial genomes
    2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 54, no 3, p. 365-375Article in journal (Refereed) Published
    Abstract [en]

    Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-90105 (URN)10.1007/s00239-001-0051-8 (DOI)11847562 (PubMedID)
    Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
    3. Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7
    Open this publication in new window or tab >>Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7
    2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 55, no 6, p. 734-744Article in journal (Refereed) Published
    Abstract [en]

    By comparing two strains of Escherichia coli (K12 and O157:H7) with an outgroup of Salmonella and Klebsiella species and analyzing the sets of genes which are present or absent in either of the three groups, we study the gene history of K12, in particular, since the respective divergences of these bacteria. Furthermore, by using a compositional method based on context bias, we evaluate not only recently imported genes but also deleted genes. In addition, we examine recent gene duplications in the two E. coli strains. It is found that turnover of DNA is high in E. coli and, more importantly, that turnover is highest for genes of low GC content. Although levels of import are high, most of the imported genes seem to be "junk" or have poorly understood functions. Nevertheless, selected genes do persist, and may even define some E. coli strains as pathogenic. Our results support the conclusion that some of the pathogenic islands in O157:H7 are likely to have been imported in recent time.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-90106 (URN)10.1007/s00239-002-2369-2 (DOI)12486532 (PubMedID)
    Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
    4. On the nature of gene innovation: Duplication patterns in microbial genomes.
    Open this publication in new window or tab >>On the nature of gene innovation: Duplication patterns in microbial genomes.
    In: Mol Biol EvolArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-90107 (URN)
    Available from: 2003-01-29 Created: 2003-01-29Bibliographically approved
    5. Duplication is more common among lateral-transfer genes
    Open this publication in new window or tab >>Duplication is more common among lateral-transfer genes
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90108 (URN)
    Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2010-01-13Bibliographically approved
  • 19.
    Hooper, Sean D
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Berg, Otto G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Detection of genes with atypical nucleotide sequence in microbial genomes2002In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 54, no 3, p. 365-375Article in journal (Refereed)
    Abstract [en]

    Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.

  • 20.
    Hooper, Sean D
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Berg, Otto G
    Duplication is more common among lateral-transfer genesManuscript (Other academic)
  • 21.
    Hooper, Sean D
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Berg, Otto G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H72002In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 55, no 6, p. 734-744Article in journal (Refereed)
    Abstract [en]

    By comparing two strains of Escherichia coli (K12 and O157:H7) with an outgroup of Salmonella and Klebsiella species and analyzing the sets of genes which are present or absent in either of the three groups, we study the gene history of K12, in particular, since the respective divergences of these bacteria. Furthermore, by using a compositional method based on context bias, we evaluate not only recently imported genes but also deleted genes. In addition, we examine recent gene duplications in the two E. coli strains. It is found that turnover of DNA is high in E. coli and, more importantly, that turnover is highest for genes of low GC content. Although levels of import are high, most of the imported genes seem to be "junk" or have poorly understood functions. Nevertheless, selected genes do persist, and may even define some E. coli strains as pathogenic. Our results support the conclusion that some of the pathogenic islands in O157:H7 are likely to have been imported in recent time.

  • 22.
    Hooper, Sean D
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Berg, Otto G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Gradients in nucleotide and codon usage along Escherichia coli genes2000In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 28, no 18, p. 3517-3523Article in journal (Refereed)
    Abstract [en]

    The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

  • 23.
    Hooper, Sean D
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Berg, Otto G
    On the nature of gene innovation: Duplication patterns in microbial genomes.In: Mol Biol EvolArticle in journal (Refereed)
  • 24.
    Martinez Barrio, Alvaro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Feifei, Xu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Lagercrantz, Erik
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    Bongcam-Rudloff, Erik
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    GeneFinder: "in silico" positional cloning of trait genesManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    Motivation: Positional cloning of trait genes is extremely laborious and the amount of information available on gene function in different organisms is increasing so rapidly that it is hard for a research group to collect all the relevant information from a number of data sources without performing a large number of manual and time consuming searches.

    Results: A web service application named GeneFinder was designed and implemented. It collects selected available information related to trait loci within a given chromosomal region that control a specific phenotype. The information contains details on gene function, disease conditions, tissue expression as well as predicted gene homologies in several other species. The information gathered is further ordered by a special-purpose ranking algorithm. A web interface to the GeneFinder web service was also developed where the results are presented in a ranked list easing its interpretation. We explain the design of the architecture, show how our web interface works, and finally test a candidate region.

    Availability: GeneFinder is publicly available and free to use. The web interface is available at http://www.genefinder.org/.

  • 25.
    Nahalkova, Jarmila
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Red fluorescent protein (DsRed2) as a novel reporter in Fusarium oxysporum f. sp. Lycopersici2003In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 225, no 2, p. 305-309Article in journal (Refereed)
    Abstract [en]

    pAn-DsRed2 vector was constructed for constitutive cytoplasmic expression of the red fluorescent protein (DsRed2) under control of the glyceraldehyde-3-phosphate dehydrogenase gene promoter from Aspergillus nidulans. DsRed2-transformation of two Fusarium oxysporum f. sp. lycopersici strains pathogenic against tomato host resulted in bright red cytoplamic fluorescence of the fungus. The transformants were screened based on the hygromycin B resistance, brightness, stability and rate of appearance of the DsRed2 fluorescence. The transormed fungi were growing normally and their pathogenicity did not change after transformation procedure. The function of novel DsRed2 marker was verified by fluorescence microscopy of the infected tomato seedlings. The results indicate that DsRed2 can be used as a efficient novel reporter gene for monitoring of the F. oxysporum within the host tissues.

  • 26.
    Nahalkova, Jarmila
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Red fluorescent protein (DsRed2) as a novel reporter in Fusarium oxysporum f. sp lycopersiei2003In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 225, no 2, p. 305-309Article in journal (Refereed)
    Abstract [en]

    pAn-DsRed2 vector was constructed for constitutive cytoplasmic expression of the red fluorescent protein (DsRed2) under control of the glyceraldehyde-3-phosphate dehydrogenase gene promoter from Aspergillus nidulans. DsRed2-transformation of two Fusarium oxysporum f. sp. lycopersici strains pathogenic against tomato host resulted in bright red cytoplamic fluorescence of the fungus. The transformants were screened based on the hygromycin B resistance, brightness, stability and rate of appearance of the DsRed2 fluorescence. The transormed fungi were growing normally and their pathogenicity did not change after transformation procedure. The function of novel DsRed2 marker was verified by fluorescence microscopy of the infected tomato seedlings. The results indicate that DsRed2 can be used as a efficient novel reporter gene for monitoring of the F oxysporum within the host tissues.

  • 27. Olivain, C
    et al.
    Humbert, C
    Nahalkova, Jarmila
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, J
    L'Haridon, F
    Alabouvette, C
    Colonization of tomato root by pathogenic and nonpathogenic Fusarium oxysporum strains inoculated together and separately into the soil2006In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 2, p. 1523-1531Article in journal (Refereed)
    Abstract [en]

    In soil, fungal colonization of plant roots has been traditionally studied by indirect methods such as microbial isolation that do not enable direct observation of infection sites or of interactions between fungal pathogens and their antagonists. Confocal laser scanning microscopy was used to visualize the colonization of tomato roots in heat-treated soil and to observe the interactions between a nonpathogenic strain, Fo47, and a pathogenic strain, Fo18, inoculated onto tomato roots in soil. When inoculated separately, both fungi colonized the entire root surface, with the exception of the apical zone. When both strains were introduced together, they both colonized the root surface and were observed at the same locations. When Fo47 was introduced at a higher concentration than Fo18, it colonized much of the root surface, but hyphae of Fo18 could still be observed at the same location on the root. There was no exclusion of the pathogenic strain by the presence of the nonpathogenic strain. These results are not consistent with the hypothesis that specific infection sites exist on the root for Fusarium oxysporum and instead support the hypothesis that competition occurs for nutrients rather than for infection sites.

  • 28. Syvänen, A.-C.
    et al.
    Amiri, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Jamal, A.
    Andersson, S. G. E.
    Kurland, C. G.
    A chimeric disposition of the elongation factor genes in Rickettsia prowazekii1996In: J. Bacteriol., Vol. 178, p. 6192-6199Article in journal (Refereed)
  • 29.
    Tamas, Ivica
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Comparative Genomics of Endosymbiotic Bacteria2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Genomes of intracellular bacteria are thought to be the products of reductive evolution. They have evolved from ancestral genomes of free-living bacteria through a process of massive gene loss. This doctoral thesis focuses on the comparison of the only two completely sequenced genomes of obligate symbionts presently available: Buchnera (Ap) and Buchnera (Sg). The sequencing of the complete genome of Buchnera (Sg) is a part of this work.

    A major finding presented is that these genomes are remarkably conserved in both genome content and gene order, which contrasts with the current view of bacterial genomes as rapidly evolving entities. On the basis of the data obtained, there are no signs of inversions, translocations, duplications or horizontally transferred genes. Furthermore, the Buchnera genomes are the first bacterial genomes identified with a loss of recA, a major gene involved in homologous recombination. This single deletion event has probably contributed to the observed genomic stasis. In addition, the recF gene involved in DNA-repair and SOS induction has also been eliminated, and mutations have started to accumulate in genes related to base-excision repair in Buchnera (Sg). In contrast to the remarkable stability in structure, surprisingly high rates of nucleotide substitutions causing amino acids replacements and substitutions at synonymous sites were identified. Therefore, the genetic changes introduced into these two genomes since their divergence is almost exclusively due to the nucleotide sequence substitutions.

    A number of pseudogenes in different stages of gene degradation have been observed in the Buchnera (Sg) genome, suggesting that genome reduction is still an ongoing, albeit slow process. Almost half of the weakly mutated genes with single or a few frameshift mutations are associated with DNA-repair, cell envelope or cysteine biosynthesis. A comparative study of a set of genes involved in peptidoglycan biosynthesis in four additional lineages of Buchnera has shown that some of the single nucleotide deletions were acquired already 30-50 million years ago. Nevertheless, the substitution patterns of these genes are typical of Buchnera genes, suggesting that they may have maintained a functional role despite the accumulation of frameshift mutations.

    The two Buchnera genomes are the first ever completely sequenced bacterial genomes for which a divergence date is available (50-70 myr). This was made possible by the availability of a fossil record for the aphid host and the exclusively vertical transmission of Buchnera via maternal inheritance. Thus, the analysis of the two genomes provides a first insight into the pace of molecular evolution in prokaryotes. Substitution rates were estimated to 9 x 10-9 synonymous substitutions per site and per year and 1.65 x 10-9 nonsynonymous substitutions per site and per year on the average for all orthologous genes identified in the genomes. The rate of gene loss was found to be surprisingly low, with about one complete gene elimination per 5-10 million years.

  • 30.
    Vinnere, Olga
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    A study of the type material of Colletotrichum fructigenumIn: Mycotaxon, ISSN 0093-4666Article in journal (Refereed)
  • 31.
    Vinnere, Olga
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Molecular characterization of two plant pathogenic Sterile White BasidiomycetesIn: European Journal of Plant Pathology, ISSN 0929-1873Article in journal (Refereed)
  • 32.
    Vinnere, Olga
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    What is Glomerella miyabeana?Manuscript (Other academic)
  • 33.
    Vinnere, Olga
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Sivasithamparam, Krishnapillai
    Gerhardson, Berndt
    A new plant pathogenic Sterile White Basidiomycete from AustraliaIn: European Journal of Plant Pathology, ISSN 0929-1873Article in journal (Refereed)
  • 34.
    Vinnere, Olga
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Wright, Sandra A.I.
    Gerhardson, Berndt
    The causal agent of anthracnose of Rhododendron in Sweden and LatviaIn: Mycological Research, ISSN 0953-7562Article in journal (Refereed)
1 - 34 of 34
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf