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Arne W. Nolte - One of the best experts on this subject based on the ideXlab platform.

Diethard Tautz - One of the best experts on this subject based on the ideXlab platform.

  • a genetic map of Cottus gobio pisces teleostei based on microsatellites can be linked to the physical map of tetraodon nigroviridis
    Journal of Evolutionary Biology, 2005
    Co-Authors: Kathryn Stemshorn, Arne W. Nolte, Diethard Tautz
    Abstract:

    To initiate QTL studies in the nonmodel fish Cottus gobio we constructed a genetic map based on 171 microsatellite markers. The mapping panel consisted of F1 intercrosses between two divergent Cottus lineages from the River Rhine System. Basic local alignment search tool (BLAST) searches with the flanking sequences of the microsatellite markers yielded a significant (e < 10−5) hit with the Tetraodon nigroviridis genomic sequence for 45% of the Cottus loci. Remarkably, most of these hits were due to short highly conserved noncoding stretches. These have an average length of 40 bp and are on average 92% conserved. Comparison of the map locations between the two genomes revealed extensive conserved synteny, suggesting that the Tetraodon genomic sequence will serve as an excellent genomic reference for at least the Acanthopterygii, which include evolutionarily interesting fish groups such as guppies (Poecilia), cichlids (Tilapia) or Xiphophorus (Platy). The apparent high density of short conserved noncoding stretches in these fish genomes will highly facilitate the identification of genes that have been identified in QTL mapping strategies of evolutionary relevant traits.

  • Direct cloning of microsatellite loci from Cottus gobio through a simplified enrichment procedure
    Molecular Ecology Notes, 2005
    Co-Authors: Arne W. Nolte, Kathryn Stemshorn, Diethard Tautz
    Abstract:

    Applying a simplified enrichment procedure, we have isolated and characterized 177 microsatellite markers for Cottus gobio L., 1758 (Cottidae, Scorpaeniformes, Teleostei). In contrast to using specific probes for the enrichment, we use genomic DNAs of unrelated organisms for cross-hybridization. This takes advantage of the fact that simple sequences are the only repetitive elements that are abundantly found in all eukaryotic genomes and that any genome usually contains all permutations of microsatellite motifs. This cross-hybridization principle was employed to enrich genomic libraries of Cottus DNA to obtain a large number of nonredundant microsatellite markers without further screening procedures.

Marie-pierre Gosselin - One of the best experts on this subject based on the ideXlab platform.

  • mesohabitat use by bullhead Cottus gobio
    Hydrobiologia, 2010
    Co-Authors: Marie-pierre Gosselin, Geoffrey E. Petts, Ian Maddock
    Abstract:

    Habitat composition and connectivity within a stream vary with changing flows but the influence of changing flow on habitat use by fish is not well understood. Meso- and microhabitat surveys were used to investigate habitat use by bullhead (Cottus gobio Linnaeus) in response to discharge variation in a small tributary of the Upper Severn, England. Mesohabitat mapping surveys were carried out over a range of summer flows (0.016–0.216 m3 s−1) and were coupled with direct underwater observations (snorkelling) of fish location. Five mesohabitat types—glides, runs, riffles, chutes and pools—were present in the reach at all flows surveyed and ‘backwaters’ were found at three flows. The macro-morphology of the reach comprised six riffle–pool sequences divided into 27 mesohabitats with the maximum diversity (23 mesohabitats) at intermediate flows (Q 43) and only 15 mesohabitats at Q 95. Despite low numbers of fish (N = 78), bullhead displayed a strong association (51% of the fish) with glides—relatively deep habitats having high rates of velocity increase with flow. However, 54% of the fish were observed in two large, persistent mesohabitats, a glide (34%) and a pool (20%), both located below a faster flowing mesohabitat. Habitat use curves based upon micro-habitat data showed bullhead favoured low velocities (<0.30 m s−1), depths less than 0.30 m and a cobble substratum. This study illustrates the value of cross-scale investigations in linking fish ecology, flow and physical habitat variability and suggests mesohabitat size, persistence and arrangement may influence fish distribution.

Nolte, Arne W. - One of the best experts on this subject based on the ideXlab platform.

  • Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish
    'Wiley', 2019
    Co-Authors: Dennenmoser Stefan, Sedlazeck, Fritz J., Schatz, Michael C., Altmueller Janine, Zytnicki Matthias, Nolte, Arne W.
    Abstract:

    Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through nonallelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genomewide distribution of transposon insertions in a young hybrid lineage (invasive Cottus, n = 11) and its parental species Cottus rhenanus (n = 17) and Cottus perifretum(n = 9) using a reference genome assembled from long single molecule pacbio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10%-197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase in novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genomewide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed overabundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected

  • Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish
    'Wiley', 2019
    Co-Authors: Dennenmoser Stefan, Sedlazeck, Fritz J., Schatz, Michael C., Zytnicki Matthias, Altmüller Janine, Nolte, Arne W.
    Abstract:

    Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through nonallelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination‐based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genomewide distribution of transposon insertions in a young hybrid lineage (“invasive Cottus”, n = 11) and its parental species Cottus rhenanus (n = 17) and Cottus perifretum (n = 9) using a reference genome assembled from long single molecule pacbio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10%–197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase in novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination‐based mechanisms rather than genomewide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed overabundance in repetitive parts of the genome suggests that generich regions are unlikely to be directly affected

  • Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish
    2018
    Co-Authors: Dennenmoser Stefan, Sedlazeck, Fritz J., Schatz, Michael C., Zytnicki Matthias, Altmüller Janine, Nolte, Arne W.
    Abstract:

    Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive Cottus”, n=11) and its parental species Cottus rhenanus (n=17) and Cottus perifretum (n=9) using a reference genome assembled from long single molecule PacBio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10 – 197 %). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase of novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genome-wide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed over-abundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected

  • Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish
    'Wiley', 2018
    Co-Authors: Dennenmoser S., Sedlazeck, Fritz J., Schatz, Michael C., Altmuller J., Zytnicki M., Nolte, Arne W.
    Abstract:

    Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage ("invasive Cottus", n=11) and its parental species Cottus rhenanus (n=17) and Cottus perifretum (n=9) using a reference genome assembled from long single molecule PacBio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10 - 197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase of novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genome-wide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed over-abundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected. This article is protected by copyright. All rights reserved

  • first_att_09_01.correctedReads.fasta
    2018
    Co-Authors: Dennenmoser Stefan, Zytnicki Matthias, Altmüller Janine, Sedlazeck Fritz, Schatz Michael, Nolte, Arne W.
    Abstract:

    PacBio genomic sequence read data (error corrected) from Cottus rhenanus

Sean M. Rogers - One of the best experts on this subject based on the ideXlab platform.

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