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Full-Text Articles in Life Sciences
Epigenetics As Driver Of Adaptation And Diversification In Microbial Eukaryotes, Agnes K.M. Weiner, Laura A. Katz
Epigenetics As Driver Of Adaptation And Diversification In Microbial Eukaryotes, Agnes K.M. Weiner, Laura A. Katz
Biological Sciences: Faculty Publications
No abstract provided.
Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, And Perhaps Also Eukaryogenesis, Adena B. Collens, Laura A. Katz
Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, And Perhaps Also Eukaryogenesis, Adena B. Collens, Laura A. Katz
Biological Sciences: Faculty Publications
Through analyses of diverse microeukaryotes, we have previously argued that eukaryotic genomes are dynamic systems that rely on epigenetic mechanisms to distinguish germline (i.e., DNA to be inherited) from soma (i.e., DNA that undergoes polyploidization, genome rearrangement, etc.), even in the context of a single nucleus. Here, we extend these arguments by including two well-documented observations: (1) eukaryotic genomes interact frequently with mobile genetic elements (MGEs) like viruses and transposable elements (TEs), creating genetic conflict, and (2) epigenetic mechanisms regulate MGEs. Synthesis of these ideas leads to the hypothesis that genetic conflict with MGEs contributed to the evolution of a …
Phylogenomics Of The Epigenetic Toolkit Reveals Punctate Retention Of Genes Across Eukaryotes, Agnes K.M. Weiner, Mario A. Cerón-Romero, Ying Yan, Laura A. Katz
Phylogenomics Of The Epigenetic Toolkit Reveals Punctate Retention Of Genes Across Eukaryotes, Agnes K.M. Weiner, Mario A. Cerón-Romero, Ying Yan, Laura A. Katz
Biological Sciences: Faculty Publications
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes …
Twisted Tales: Insights Into Genome Diversity Of Ciliates Using Single-Cell ‘Omics, Maurer-Alcala X. Xyrus X. Maurer-Alcala, Ying Yan, Olivia A. Pilling, Rob Knight, Laura A. Katz
Twisted Tales: Insights Into Genome Diversity Of Ciliates Using Single-Cell ‘Omics, Maurer-Alcala X. Xyrus X. Maurer-Alcala, Ying Yan, Olivia A. Pilling, Rob Knight, Laura A. Katz
Biological Sciences: Faculty Publications
The emergence of robust single-cell ‘omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell ‘omics approaches show: 1) the description of the ciliates in the class Karyorelictea as “primitive”is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani’s (1890) observation …
The Dynamic Nature Of Genomes Across The Tree Of Life, Angela M. Oliverio, Laura A. Katz
The Dynamic Nature Of Genomes Across The Tree Of Life, Angela M. Oliverio, Laura A. Katz
Biological Sciences: Faculty Publications
Genomes are dynamic in lineages across the tree of life. Among bacteria and archaea, for example, DNA content varies through out life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. These observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. Here, we synthesize information on three aspects of dynamic genomes from exemplars representing a diverse array of bacterial and archaeal lineages: 1) ploidy level variation, 2) epigenetic mechanisms, and 3) life cycle variation. …
On The Nature Of Species: Insights From Paramecium And Other Ciliates, Meaghan S. Hall, Laura A. Katz
On The Nature Of Species: Insights From Paramecium And Other Ciliates, Meaghan S. Hall, Laura A. Katz
Biological Sciences: Faculty Publications
The multiple species concepts currently in use by the scientific community (e. g. Morphological, Biological, Phylogenetic) are united in that they all aim to capture the process of divergence between populations. For example, the Biological Species Concept defines a species as a natural group of organisms that is reproductively isolated from other such groups. Here we synthesize nearly a century of research on the ciliate genus Paramecium that highlights the shortcomings of our prevailing notions on the nature of species. In this lineage, there is discordance between morphology, mating behavior, and genetics, features assumed to be correlated, at least after …
The Dynamic Nature Of Eukaryotic Genomes, Laura Wegener Parfrey, Daniel J.G. Lahr, Laura A. Katz
The Dynamic Nature Of Eukaryotic Genomes, Laura Wegener Parfrey, Daniel J.G. Lahr, Laura A. Katz
Biological Sciences: Faculty Publications
Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in …