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  1. Article ; Online: Gene flow and species boundaries of the genus

    Cobo-Simón, Marta / Hart, Rowan / Ochman, Howard

    mSystems

    2023  Volume 8, Issue 4, Page(s) e0029223

    Abstract: ... The ... ...

    Abstract The genus
    MeSH term(s) Animals ; Phylogeny ; Gene Flow ; Salmonella/genetics ; Salmonella enterica/genetics ; Nucleotides
    Chemical Substances Nucleotides
    Language English
    Publishing date 2023-07-24
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 2379-5077
    ISSN (online) 2379-5077
    DOI 10.1128/msystems.00292-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Escherichia Coli: What Is and Which Are?

    Cobo-Simón, Marta / Hart, Rowan / Ochman, Howard

    Molecular biology and evolution

    2023  Volume 40, Issue 1

    Abstract: Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and ... ...

    Abstract Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the biological species concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent, and objective principle that allows species-level classification across all domains of life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1,887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups, or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.
    MeSH term(s) Escherichia coli/genetics ; Phylogeny ; Shigella/genetics ; Genome ; Base Sequence ; Genome, Bacterial
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msac273
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa.

    Cobo-Simón, Marta / Tamames, Javier

    BMC genomics

    2017  Volume 18, Issue 1, Page(s) 499

    Abstract: Background: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput ... ...

    Abstract Background: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences.
    Results: To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions.
    Conclusions: Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments.
    Language English
    Publishing date 2017-06-29
    Publishing country England
    Document type Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-017-3888-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes.

    Tamames, Javier / Cobo-Simón, Marta / Puente-Sánchez, Fernando

    BMC genomics

    2019  Volume 20, Issue 1, Page(s) 960

    Abstract: Background: Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw ...

    Abstract Background: Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.
    Results: We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled).
    Conclusions: Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.
    MeSH term(s) Algorithms ; Cluster Analysis ; Computational Biology/methods ; Metagenome/genetics ; Metagenomics ; Molecular Sequence Annotation/methods ; Sequence Analysis, DNA
    Language English
    Publishing date 2019-12-10
    Publishing country England
    Document type Comparative Study ; Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-019-6289-6
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  5. Article ; Online: Cenozoic tectonic and climatic events in southern Iberian Peninsula: Implications for the evolutionary history of freshwater fish of the genus Squalius (Actinopterygii, Cyprinidae).

    Perea, Silvia / Cobo-Simon, Marta / Doadrio, Ignacio

    Molecular phylogenetics and evolution

    2016  Volume 97, Page(s) 155–169

    Abstract: Southern Iberian freshwater ecosystems located at the border between the European and African plates represent a tectonically complex region spanning several geological ages, from the uplifting of the Betic Mountains in the Serravalian-Tortonian periods ... ...

    Abstract Southern Iberian freshwater ecosystems located at the border between the European and African plates represent a tectonically complex region spanning several geological ages, from the uplifting of the Betic Mountains in the Serravalian-Tortonian periods to the present. This area has also been subjected to the influence of changing climate conditions since the Middle-Upper Pliocene when seasonal weather patterns were established. Consequently, the ichthyofauna of southern Iberia is an interesting model system for analyzing the influence of Cenozoic tectonic and climatic events on its evolutionary history. The cyprinids Squalius malacitanus and Squalius pyrenaicus are allopatrically distributed in southern Iberia and their evolutionary history may have been defined by Cenozoic tectonic and climatic events. We analyzed MT-CYB (510 specimens) and RAG1 (140 specimens) genes of both species to reconstruct phylogenetic relationships and to estimate divergence times and ancestral distribution ranges of the species and their populations. We also assessed their levels of genetic structure and diversity as well as the amount of gene flow between populations. To investigate recent paleogeographical and climatic factors in southern Iberia, we modeled changes-through-time in sea level from the LGM to the present. Phylogenetic, geographic and population structure analyses revealed two well-supported species (S. malacitanus and S. pyrenaicus) in southern Iberia and two subclades (Atlantic and Mediterranean) within S. malacitanus. The origin of S. malacitanus and the separation of its Atlantic and Mediterranean populations occurred during the Serravalian-Tortonian and Miocene-Pliocene periods, respectively. These divergence events occurred in the Middle Pliocene and Pleistocene in S. pyrenaicus. In both species, Atlantic basins possessed populations with higher genetic diversity than Mediterranean, which may be explained by the Janda Lagoon. The isolation of S. malacitanus was earlier and related to the rising of the Betic Mountains. Divergence of its Atlantic and Mediterranean populations was associated with the creation of the freshwater systems of southern Iberia close to the Gibraltar Strait. The presence of S. pyrenaicus in southern Iberia may be the result of recent colonization associated with river capture, as demonstrated our biogeographic reconstruction.
    MeSH term(s) Animals ; Atlantic Ocean ; Climate ; Cyprinidae/genetics ; Ecosystem ; Evolution, Molecular ; Fresh Water ; Gene Flow/genetics ; Genes, Mitochondrial/genetics ; Genetic Variation ; History, Ancient ; Mediterranean Sea ; Phylogeny ; Phylogeography ; Rivers ; Spain
    Language English
    Publishing date 2016-04
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2016.01.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3644: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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