Biology subjects

Katz, L. A.

Publications and source records attributed to Katz, L. A..

9 recordsLinked to original sources

bioRxiv2026

Elucidating changes in gene expression driving nuclear dynamics across a foraminiferal life cycle with Pheno2Seq

In many microeukaryotes, conserved morphology masks transitions between haploid and diploid phases of the life cycle, making it difficult to link gene expression to development. Hence, insights on such transitions come largely from model lineages of animals, plants and fungi. To address this gap, we developed a method, Pheno2Seq, that enables visualization of fluorescently-stained individuals followed by identification of candidate genes through single-cell transcriptome analyses. We applied this method in Allogromia laticollaris, a foraminifera with a complex life cycle that alternates between haploid and diploid phases and includes endoreplication to ~11,000N. As this taxon lacks a reference genome, we used a conservative phylogenomic approach to identify gene families present across diverse foraminifera. We identified >800 differentially expressed genes underlying life cycle transitions along with a similar number of constitutively-expressed genes. During Zerfall, a phase of extreme endoreplication, the transcriptome is largely silenced with the exception of gene families involved in genome processes and stability. Intriguingly, these gene families include chromatin modifiers, spliceosomal components and histone paralogs, some of which are known to contribute to cell type differentiation in multicellular eukaryotes. We also find numerous genes involved in DNA repair (e.g. DNA damage response and R-loop regulating genes). We speculate that these genes are part of an ancient eukaryotic toolkit, likely present in the last eukaryotic common ancestor (LECA) and that regulates genomes during life cycle transitions. Our method, Pheno2Seq, can be adapted to diverse lineages to enable the study of life cycle regulation in microeukaryotes that lack morphologically distinguishable life cycle stages.

evolutionary biology↗

bioRxiv2025

A new class of proteinaceous biomaterial with unprecedented properties in unicellular eukaryotes

Biomaterials fundamentally reshape material use, providing superior properties and sustainable alternatives relevant to medicine, textiles, and high-tech applications. Research mainly focuses on animal-derived proteinaceous biomaterials, which remain challenging to reproduce while retaining their remarkable properties. We discovered that the shells of tintinnid ciliates, a group of planktonic unicellular eukaryotes, are composed of self-assembling structural proteins. The shells form in water, are structurally diverse, and show exceptional resistance against high temperatures and the strongest chemicals. Combining single-cell transcriptomics and mass-spectrometry of the shells, we identified the amino acid sequences of the shell-forming proteins. They are exceptionally rich in aromatic residues and possess a unique architecture with flexible, unfolded segments connecting highly stable beta-sheets. This easily accessible system promises new aspects to advance current biomaterial design.

molecular biology↗

bioRxiv2025

A geothermal amoeba sets a new upper temperature limit for eukaryotes

The study of temperature limits has transformed our knowledge of the boundaries of life but has been largely focused on bacteria and archaea. We isolated a novel geothermal amoeba, Incendiamoeba cascadensis, that divides at 63{degrees}C (145.4{degrees}F), establishing a new record for the upper temperature limit across all eukaryotes. We demonstrated cellular proliferation with growth experiments and visualized mitosis via expansion microscopy. Using high-temperature live-cell imaging, we quantified movement up to 64{degrees}C. We assembled the genome of I. cascadensis and using comparative genomics found an enrichment of genes related to proteostasis, genome stability, and sensing the external environment. Taken together, our findings challenge the current paradigm of temperature constraints on eukaryotic cells and reshape our understanding of where and how eukaryotic life can persist.

microbiology↗

bioRxiv2024

Protists as mediators of complex microbial and viral associations

Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae, and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.

microbiology↗

bioRxiv2024

Genome content in the non-model ciliate Chilodonella uncinata: insights into nuclear architecture, gene-sized chromosomes among the total DNA in their somatic macronuclei during their development

Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following sex (i.e., conjugation). Nuclear developmental stages are not as well explored among non-model ciliate genera, including Chilodonella uncinata (Class-Phyllopharyngea), the focus of our work. Here, we characterize nuclear architecture and genome dynamics in C. uncinata by combining DAPI (4',6-diamidino-2-phenylindole) staining and fluorescence in situ hybridization (FISH) techniques with confocal microscopy. We developed a telomere probe for staining alongside DAPI, which allows for the identification of fragmented somatic chromosomes among the total DNA in the nuclei. We quantify both total DNA and telomere-bound signals to explore changes in DNA content and chromosome maturation across Chilodonellas nuclear life cycle. Specifically, we find that MAC developmental stages in the ciliate C. uncinata are different than the data reported from other ciliate species. These data provide insights into nuclear dynamics during nuclear development and enrich our understanding of genome evolution in non-model ciliates.

developmental biology↗

bioRxiv2024

Rethinking large scale phylogenomics with PhyloToL 6, a flexible toolkit to enable phylogeny-informed data curation and analysis

Eukaryotic diversity is largely microbial, with macroscopic lineages (plant, animals and fungi) nesting among a plethora of diverse protists. Understanding the evolutionary relationships among eukaryotes is rapidly advancing through omics analyses, but phylogenomics are challenging for microeukaryotes, particularly uncultivable lineages, as single-cell sequencing approaches generate a mixture of sequences from hosts, associated microbiomes, and contaminants. Moreover, many analyses of eukaryotic gene families and phylogenies rely on boutique datasets and methods that are challenging for other research groups to replicate. To address these challenges, we present EukPhylo v1.0, a modular, user-friendly pipeline that enables effective data curation through phylogeny-informed contamination removal, estimation of homologous gene families (GFs), and generation of both multisequence alignments and gene trees. Analyses can use a hook database of [~]15k ancient GFs or users can easily replace this hook with a set of gene families of interest. We demonstrate the power of EukPhylo, including a suite of stand-alone utilities, through analyses of 500 conserved GFs sampled from 1,000 diverse species of eukaryotes, bacteria and archaea. We show improvements in estimates of the eukaryotic tree of life, recovering clades that are well established in the literature, through successive rounds of curation using the EukPhylo contamination loop. The final trees corroborate numerous hypotheses in the literature (e.g. Opisthokonta, Rhizaria, Amoebozoa) while challenging others (e.g. CRuMs, Obazoa, Diaphoretickes). We believe that the flexibility and transparency of EukPhylo sets standards for curation of omics data for future studies. AUTHOR SUMMARYThe majority of eukaryotic lineages are microbial, with plants and animals nesting among diverse amoeba, flagellates, and other predominantly-microbial clades. Yet analyses of the evolution of microbial eukaryotes is hampered by the lack of tools for efficient analysis of genome-scaled data, especially in light of the genome complexity and high levels of contamination associated with these microorganism. Furthermore, many existing analyses rely on boutique datasets and decision making that lacks transparency and are thus difficult for others to repeat. To address these challenges, we present EukPhylo as an easy-to-use toolkit that fills a gap in phylogenomic methods, and we analyze of 500 gene families from 1,000 species to demonstrate the power of this approach in estimating the eukaryotic tree of life. EukPhylo enables exploration of eukaryotic evolution in a manner that is both transparent and easily repeatable, and hence can be used to illuminate the origin and diversification of eukaryotic life on Earth.

evolutionary biology↗

bioRxiv2024

Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes

Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.

evolutionary biology↗

bioRxiv2021

Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

Advances in phylogenetics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree - species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root. Impact summaryFinding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes. But this is one of the most challenging questions in evolutionary biology because the age (~1.8 billion years), diversity and complexity of eukaryotes challenge phylogenomic methods. This study evaluates the root using reconciliation of gene trees and species trees instead of the more common approach of analyzing concatenated genes. The dataset used in this study is bigger and more taxonomically inclusive than the dataset of any previous study about the eukaryotic root, and supports a root at or within Opisthokonta (e.g. animals and fungi). Finally, we explicitly test alternative hypotheses from the literature, and again find support for an Opisthokonta root.

evolutionary biology↗

bioRxiv2018

Genome analysis of the unicellular eukaryote Euplotes vannus provides insights into mating type determination and tolerance to environmental stresses

As a model organism in studies of cell and environmental biology, the free-living and cosmopolitan ciliated protist Euplotes vannus has more than ten mating types (sexes) and shows strong resistance to environmental stresses. However, the molecular basis of its sex determination mechanism and how the cell responds to stress remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronucleus (MAC; i.e. somatic) genome and partial micronucleus (MIC; i.e. germline) genome of Euplotes vannus. Furthermore, MAC genomic and transcriptomic data from several mating types of E. vannus were investigated and gene expression levels were profiled under different environmental stresses, including nutrient scarcity, extreme temperature, salinity and the presence of free ammonia. We found that E. vannus, which possesses gene-sized nanochromosomes in its MAC, shares a similar pattern on frameshifting and stop codon usage as Euplotes octocarinatus and may be undergoing incipient sympatric speciation with Euplotes crassus. Somatic pheromone loci of E. vannus are generated from programmed DNA rearrangements of multiple germline macronuclear destined sequences (MDS) and the mating types of E. vannus are distinguished by the different combinations of pheromone loci instead of possessing mating type-specific genes. Lastly, we linked the resilience to environmental temperature change to the evolved loss of temperature stress-sensitive regulatory regions of HSP70 gene in E. vannus. Together, the genome resources generated in this study, which are available online at Euplotes vannus DB (http://evan.ciliate.org), provide new evidence for sex determination mechanism in eukaryotes and common pheromone-mediated cell-cell signaling and cross-mating.

genomics↗