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Full-Text Articles in Life Sciences
Foraminifera As A Model Of Eukaryotic Genome Dynamism, Caitlin Timmons, Kristine Le, H. B. Rappaport, Elinor G. Sterner, Xyrus X. Maurer-Alcaláh, Susan T. Goldstein, Laura A. Katz
Foraminifera As A Model Of Eukaryotic Genome Dynamism, Caitlin Timmons, Kristine Le, H. B. Rappaport, Elinor G. Sterner, Xyrus X. Maurer-Alcaláh, Susan T. Goldstein, Laura A. Katz
Biological Sciences: Faculty Publications
In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual’s life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of Allogromia laticollaris strain Cold Spring Harbor (CSH), one of …
Phylotol: A Taxon/Gene-Rich Phylogenomic Pipeline To Explore Genome Evolution Of Diverse Eukaryotes, Mario A. Cerón-Romero, Xyrus X. Maurer-Alcalá, Jean David Grattepanche, Ying Yan, Miguel M. Fonseca, Laura A. Katz, Fabia Ursula Battistuzz
Phylotol: A Taxon/Gene-Rich Phylogenomic Pipeline To Explore Genome Evolution Of Diverse Eukaryotes, Mario A. Cerón-Romero, Xyrus X. Maurer-Alcalá, Jean David Grattepanche, Ying Yan, Miguel M. Fonseca, Laura A. Katz, Fabia Ursula Battistuzz
Biological Sciences: Faculty Publications
Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation …
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 …
Nuclear Architecture And Patterns Of Molecular Evolution Are Correlated In The Ciliate Chilodonella Uncinata, Xyrus X. Maurer-Alcalá, Laura A. Katz
Nuclear Architecture And Patterns Of Molecular Evolution Are Correlated In The Ciliate Chilodonella Uncinata, Xyrus X. Maurer-Alcalá, Laura A. Katz
Biological Sciences: Faculty Publications
The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. …
Genome Structure Drives Patterns Of Gene Family Evolution In Ciliates, A Case Study Using Chilodonella Uncinata (Protista, Ciliophora, Phyllopharyngea), Feng Gao, Weibo Song, Laura A. Katz
Genome Structure Drives Patterns Of Gene Family Evolution In Ciliates, A Case Study Using Chilodonella Uncinata (Protista, Ciliophora, Phyllopharyngea), Feng Gao, Weibo Song, Laura A. Katz
Biological Sciences: Faculty Publications
In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata …
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 …