The Experts below are selected from a list of 154734 Experts worldwide ranked by ideXlab platform

Lizhi Gao - One of the best experts on this subject based on the ideXlab platform.

  • rapid and recent Evolution of ltr retrotransposons drives rice Genome Evolution during the speciation of aa Genome oryza species
    G3: Genes Genomes Genetics, 2017
    Co-Authors: Qunjie Zhang, Lizhi Gao
    Abstract:

    The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to Genome Evolution during plant speciation have remained largely unanswered. Here, we perform a Genome-wide comparison of all eight Oryza AA-Genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive Evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific Evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid Evolution of LTR retrotransposons not only divergently shaped the architecture of rice Genomes but also contributed to the process of speciation and diversification of rice.

  • rapid and recent Evolution of ltr retrotransposons drives rice Genome Evolution during the speciation of aa Genome oryza species
    bioRxiv, 2016
    Co-Authors: Qunjie Zhang, Lizhi Gao
    Abstract:

    The dynamics of LTR retrotransposons and their contribution to Genome Evolution during plant speciation have remained largely unanswered. Here, we perform a Genome-wide comparison of all eight Oryza AA- Genome species, and identify 3,911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ~4.8 Myr. Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive Evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific Evolution. The estimated insertion times of 2,213 complete retrotransposons from the top 23 most abundant families reveal divergent life-histories marked by speedy accumulation, decline and extinction that differed radically between species. We hypothesize that this rapid Evolution of LTR retrotransposons not only divergently shaped the architecture of rice Genomes but also contributed to the process of speciation and diversification of rice.

John S Sproul - One of the best experts on this subject based on the ideXlab platform.

  • repetitive dna profiles reveal evidence of rapid Genome Evolution and reflect species boundaries in ground beetles
    Systematic Biology, 2020
    Co-Authors: John S Sproul, Lindsey M Barton, David R Maddison
    Abstract:

    Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the Genome's component parts. Comparative study of entire Genome architecture in model organisms is shedding light on mechanisms underlying Genome regulation, Evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for Evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the Genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the Genome, revealing evidence of rapid Genome Evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the Evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the Genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and Genome Evolution. [Bembidion; Carabidae; copy number variation profiles; rapid Genome Evolution; ribosomal DNA; species delimitation.].

  • repetitive dna profiles reveal evidence of rapid Genome Evolution and reflect species boundaries in ground beetles
    bioRxiv, 2020
    Co-Authors: John S Sproul, Lindsey M Barton, David R Maddison
    Abstract:

    Abstract Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the Genome’s component parts. Comparative study of entire Genome architecture in model organisms is shedding light on mechanisms underlying Genome regulation, Evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for Evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the Genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the Genome, revealing evidence of rapid Genome Evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the Evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the Genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and Genome Evolution.

Vincent Daubin - One of the best experts on this subject based on the ideXlab platform.

  • reductive Genome Evolution at both ends of the bacterial population size spectrum
    Nature Reviews Microbiology, 2014
    Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel A B Marais, Vincent Daubin
    Abstract:

    Bacterial Genomes show substantial variations in size. The smallest bacterial Genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive Genome reduction and show patterns consistent with degenerative processes predicted to occur in species with small effective population sizes. However, similar Genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. Here, we discuss the various hypotheses that have been put forward to account for this reductive Genome Evolution at both ends of the spectrum of bacterial population size.

  • reductive Genome Evolution at both ends of the bacterial population size spectrum
    Nature Reviews Microbiology, 2014
    Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel A B Marais, Vincent Daubin
    Abstract:

    Bacterial Genomes show substantial variations in size. The smallest bacterial Genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive Genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar Genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive Genome Evolution at both ends of the bacterial population size spectrum.

Bérénice Batut - One of the best experts on this subject based on the ideXlab platform.

  • reductive Genome Evolution at both ends of the bacterial population size spectrum
    Nature Reviews Microbiology, 2014
    Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel A B Marais, Vincent Daubin
    Abstract:

    Bacterial Genomes show substantial variations in size. The smallest bacterial Genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive Genome reduction and show patterns consistent with degenerative processes predicted to occur in species with small effective population sizes. However, similar Genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. Here, we discuss the various hypotheses that have been put forward to account for this reductive Genome Evolution at both ends of the spectrum of bacterial population size.

  • reductive Genome Evolution at both ends of the bacterial population size spectrum
    Nature Reviews Microbiology, 2014
    Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel A B Marais, Vincent Daubin
    Abstract:

    Bacterial Genomes show substantial variations in size. The smallest bacterial Genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive Genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar Genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive Genome Evolution at both ends of the bacterial population size spectrum.

David R Maddison - One of the best experts on this subject based on the ideXlab platform.

  • repetitive dna profiles reveal evidence of rapid Genome Evolution and reflect species boundaries in ground beetles
    Systematic Biology, 2020
    Co-Authors: John S Sproul, Lindsey M Barton, David R Maddison
    Abstract:

    Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the Genome's component parts. Comparative study of entire Genome architecture in model organisms is shedding light on mechanisms underlying Genome regulation, Evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for Evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the Genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the Genome, revealing evidence of rapid Genome Evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the Evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the Genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and Genome Evolution. [Bembidion; Carabidae; copy number variation profiles; rapid Genome Evolution; ribosomal DNA; species delimitation.].

  • repetitive dna profiles reveal evidence of rapid Genome Evolution and reflect species boundaries in ground beetles
    bioRxiv, 2020
    Co-Authors: John S Sproul, Lindsey M Barton, David R Maddison
    Abstract:

    Abstract Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the Genome’s component parts. Comparative study of entire Genome architecture in model organisms is shedding light on mechanisms underlying Genome regulation, Evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for Evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the Genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the Genome, revealing evidence of rapid Genome Evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the Evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the Genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and Genome Evolution.