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Rappaport HB, Oliverio AM. Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life. Genome Biol Evol 2024; 16:evae160. [PMID: 39101574 PMCID: PMC11299111 DOI: 10.1093/gbe/evae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2024] [Indexed: 08/06/2024] Open
Abstract
From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.
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Affiliation(s)
- H B Rappaport
- Department of Biology, Syracuse University, Syracuse, NY, USA
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2
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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
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.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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Maurer-Alcalá XX, Cote-L’Heureux A, Kosakovsky Pond SL, Katz LA. Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates. PLoS One 2024; 19:e0291688. [PMID: 38271450 PMCID: PMC10810533 DOI: 10.1371/journal.pone.0291688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 09/02/2023] [Indexed: 01/27/2024] Open
Abstract
The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution of de novo genes in model species. Here we explore the origins of lineage-specific genes in ciliates, a ~1 billion year old clade of microeukaryotes that are defined by their division of somatic and germline functions into distinct nuclei. Previous analyses on conserved gene families have shown the effect of ciliates' unusual genome architecture on gene family evolution: extensive genome processing-the generation of thousands of gene-sized somatic chromosomes from canonical germline chromosomes-is associated with larger and more diverse gene families. To further study the relationship between ciliate genome architecture and gene family evolution, we analyzed lineage specific gene families from a set of 46 transcriptomes and 12 genomes representing x species from eight ciliate classes. We assess how the evolution lineage-specific gene families occurs among four groups of ciliates: extensive fragmenters with gene-size somatic chromosomes, non-extensive fragmenters with "large'' multi-gene somatic chromosomes, Heterotrichea with highly polyploid somatic genomes and Karyorelictea with 'paradiploid' somatic genomes. Our analyses demonstrate that: 1) most lineage-specific gene families are found at shallow taxonomic scales; 2) extensive genome processing (i.e., gene unscrambling) during development likely influences the size and number of young lineage-specific gene families; and 3) the influence of somatic genome architecture on molecular evolution is increasingly apparent in older gene families. Altogether, these data highlight the influences of genome architecture on the evolution of lineage-specific gene families in eukaryotes.
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Affiliation(s)
- Xyrus X. Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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4
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Weiner AKM, Sehein T, Cote-L’Heureux A, Sleith RS, Greco M, Malekshahi C, Ryan-Embry C, Ostriker N, Katz LA. Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes. Evolution 2023; 77:2472-2483. [PMID: 37672006 PMCID: PMC10629589 DOI: 10.1093/evolut/qpad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies-Hyalosphenia papilio and Hyalosphenia elegans-of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor Sehein
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Robin S Sleith
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Mattia Greco
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Clara Malekshahi
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Chase Ryan-Embry
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Naomi Ostriker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, United States
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5
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Rappaport HB, Oliverio AM. Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology. Nat Commun 2023; 14:4959. [PMID: 37587119 PMCID: PMC10432404 DOI: 10.1038/s41467-023-40657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Research in extreme environments has substantially expanded our understanding of the ecology and evolution of life on Earth, but a major group of organisms has been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies of protists in extreme environments and identify focal lineages that are of significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, and Cryptophyta. We argue that extreme environments are prime sampling targets to fill gaps in the eukaryotic tree of life and to increase our understanding of the ecology, metabolism, genome architecture, and evolution of eukaryotic life.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Biology, Syracuse University, Syracuse, NY, 13210, USA.
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Singh A, Maurer‐Alcalá XX, Solberg T, Häußermann L, Gisler S, Ignarski M, Swart EC, Nowacki M. Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium. EMBO J 2022; 41:e111839. [PMID: 36221862 PMCID: PMC9670198 DOI: 10.15252/embj.2022111839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 01/13/2023] Open
Abstract
Small RNAs mediate the silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. The unicellular ciliate Paramecium is a model to study dynamic genome organization in eukaryotic cells, given its unique feature of nuclear dimorphism. Here, the formation of the somatic macronucleus during sexual reproduction requires eliminating thousands of transposon remnants (IESs) and transposable elements scattered throughout the germline micronuclear genome. The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries. Here we show that IES recognition and precise excision are facilitated by recruiting ISWI1, a Paramecium homolog of the chromatin remodeler ISWI. ISWI1 knockdown substantially inhibits DNA elimination, quantitatively similar to development-specific sRNA gene knockdowns but with much greater aberrant IES excision at alternative boundaries. We also identify key development-specific sRNA biogenesis and transport proteins, Ptiwi01 and Ptiwi09, as ISWI1 cofactors in our co-immunoprecipitation studies. Nucleosome profiling indicates that increased nucleosome density correlates with the requirement for ISWI1 and other proteins necessary for IES excision. We propose that chromatin remodeling together with small RNAs is essential for efficient and precise DNA elimination in Paramecium.
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Affiliation(s)
- Aditi Singh
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
| | | | - Therese Solberg
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | | | - Silvan Gisler
- Institute of Cell BiologyUniversity of BernBernSwitzerland
| | | | - Estienne C Swart
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
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Cerón-Romero MA, Fonseca MM, de Oliveira Martins L, Posada D, Katz LA. Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages. Genome Biol Evol 2022; 14:evac119. [PMID: 35880421 PMCID: PMC9366629 DOI: 10.1093/gbe/evac119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Advances in phylogenomics 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 does not consider phylogenetically-informative events like gene duplications and losses. A recent study using gene tree parsimony (GTP) suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we use GTP with a duplication-loss model in a gene-rich and taxon-rich dataset (i.e., 2,786 gene families from two sets of 155 and 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We also contrasted our results and discarded alternative hypotheses from the literature using GTP and the likelihood-based method SpeciesRax. Our estimates suggest a root between Fungi or Opisthokonta and all other eukaryotes; but based on further analysis of genome size, we propose that the root between Opisthokonta and all other eukaryotes is the most likely.
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Affiliation(s)
- Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Miguel M Fonseca
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Leonardo de Oliveira Martins
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Smith SA, Santoferrara LF, Katz LA, McManus GB. Genome architecture used to supplement species delineation in two cryptic marine ciliates. Mol Ecol Resour 2022; 22:2880-2896. [PMID: 35675173 DOI: 10.1111/1755-0998.13664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.
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Cote-L’Heureux A, Maurer-Alcalá XX, Katz LA. Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events. PLoS Genet 2022; 18:e1010239. [PMID: 35731825 PMCID: PMC9255765 DOI: 10.1371/journal.pgen.1010239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/05/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022] Open
Abstract
Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.
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Affiliation(s)
- Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | | | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Program in Organismic Biology and Evolution, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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Velle KB, Kennard AS, Trupinić M, Ivec A, Swafford AJM, Nolton E, Rice LM, Tolić IM, Fritz-Laylin LK, Wadsworth P. Naegleria's mitotic spindles are built from unique tubulins and highlight core spindle features. Curr Biol 2022; 32:1247-1261.e6. [PMID: 35139359 PMCID: PMC9036621 DOI: 10.1016/j.cub.2022.01.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/02/2021] [Accepted: 01/12/2022] [Indexed: 12/30/2022]
Abstract
Naegleria gruberi is a unicellular eukaryote whose evolutionary distance from animals and fungi has made it useful for developing hypotheses about the last common eukaryotic ancestor. Naegleria amoebae lack a cytoplasmic microtubule cytoskeleton and assemble microtubules only during mitosis and thus represent a unique system for studying the evolution and functional specificity of mitotic tubulins and the spindles they assemble. Previous studies show that Naegleria amoebae express a divergent α-tubulin during mitosis, and we now show that Naegleria amoebae express a second mitotic α- and two mitotic β-tubulins. The mitotic tubulins are evolutionarily divergent relative to typical α- and β-tubulins and contain residues that suggest distinct microtubule properties. These distinct residues are conserved in mitotic tubulin homologs of the "brain-eating amoeba" Naegleria fowleri, making them potential drug targets. Using quantitative light microscopy, we find that Naegleria's mitotic spindle is a distinctive barrel-like structure built from a ring of microtubule bundles. Similar to those of other species, Naegleria's spindle is twisted, and its length increases during mitosis, suggesting that these aspects of mitosis are ancestral features. Because bundle numbers change during metaphase, we hypothesize that the initial bundles represent kinetochore fibers and secondary bundles function as bridging fibers.
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Affiliation(s)
- Katrina B Velle
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Andrew S Kennard
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Monika Trupinić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Arian Ivec
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, 10000 Zagreb, Croatia
| | - Andrew J M Swafford
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Emily Nolton
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lillian K Fritz-Laylin
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA.
| | - Patricia Wadsworth
- Department of Biology, University of Massachusetts, 611 N. Pleasant Street, Amherst, MA 01003, USA.
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11
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Weiner AKM, Cullison B, Date SV, Tyml T, Volland JM, Woyke T, Katz LA, Sleith RS. Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods. Protist 2022; 173:125853. [PMID: 35030517 PMCID: PMC9148389 DOI: 10.1016/j.protis.2021.125853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/22/2021] [Accepted: 12/09/2021] [Indexed: 02/03/2023]
Abstract
Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic signal across sampling sites. Fluorescence and transmission electron microscopy showed the presence of intact algae cells within the amoeba cell. Yet analysis of transcriptome data suggested that the algal nuclei are inactive, implying that instead of a stable, mutualistic relationship, the algae may be temporarily exploited for photosynthetic activity before being digested. Differences in gene expression of H. papilio and Hyalosphenia elegans demonstrated increased expression of genes related to oxidative stress. Together, our analyses increase knowledge of this host-symbiont association and reveal 1) higher diversity of associated algae than previously characterized, 2) a transient association between H. papilio and Chlorella with unclear benefits for the algae, 3) algal-induced gene expression changes in the host.
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Affiliation(s)
- Agnes K M Weiner
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA; NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Jahnebakken 5, 5007 Bergen, Norway
| | - Billie Cullison
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
| | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
| | - Tomáš Tyml
- Laboratory for Research in Complex Systems, Menlo Park, California, USA; DOE Joint Genome Institute, Berkeley, California, USA
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, California, USA; DOE Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, California, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Robin S Sleith
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA.
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Weiner AKM, Cerón-Romero MA, Yan Y, Katz LA. Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes. Genome Biol Evol 2021; 12:2196-2210. [PMID: 33049043 DOI: 10.1093/gbe/evaa198] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
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 and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
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Irisarri I, Strassert JFH, Burki F. Phylogenomic Insights into the Origin of Primary Plastids. Syst Biol 2021; 71:105-120. [PMID: 33988690 DOI: 10.1093/sysbio/syab036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and non-monophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic datasets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual datasets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear datasets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and revealed a putative association with plastid-lacking Picozoa. This study represents an important step towards better understanding deep eukaryotic evolution and the origin of plastids.
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Affiliation(s)
- Iker Irisarri
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Jürgen F H Strassert
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Science For Life Laboratory, Uppsala University, 75236 Sweden
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14
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Mao Y, Hou S, Shi J, Economo EP. TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data. Mol Ecol Resour 2020; 20. [PMID: 32073732 DOI: 10.1111/1755-0998.13149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 11/30/2022]
Abstract
Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python-TREEasy-that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree and RaxML-NG), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the "WGD clade" of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).
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Affiliation(s)
- Yafei Mao
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Siqing Hou
- Cognitive Neurorobotics Research Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Junfeng Shi
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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15
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Ribeiro GM, Porfírio-Sousa AL, Maurer-Alcalá XX, Katz LA, Lahr DJG. De novo Sequencing, Assembly, and Annotation of the Transcriptome for the Free-Living Testate Amoeba Arcella intermedia. J Eukaryot Microbiol 2020; 67:383-392. [PMID: 31971327 DOI: 10.1111/jeu.12788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/19/2019] [Accepted: 12/22/2019] [Indexed: 11/29/2022]
Abstract
Arcella, a diverse understudied genus of testate amoebae is a member of Tubulinea in Amoebozoa group. Transcriptomes are a powerful tool for characterization of these organisms as they are an efficient way of characterizing the protein-coding potential of the genome. In this work, we employed both single-cell and clonal populations transcriptomics to create a reference transcriptome for Arcella. We compared our results with annotations of Dictyostelium discoideum, a model Amoebozoan. We assembled a pool of 38 Arcella intermedia transcriptomes, which after filtering are composed of a total of 14,712 translated proteins. There are GO categories enriched in Arcella including mainly intracellular signal transduction pathways; we also used KEGG to annotate 11,546 contigs, which also have similar distribution to Dictyostelium. A large portion of data is still impossible to assign to a gene family, probably due to a combination of lineage-specific genes, incomplete sequences in the transcriptome and rapidly evolved genes. Some absences in pathways could also be related to low expression of these genes. We provide a reference database for Arcella, and we highlight the emergence of the need for further gene discovery in Arcella.
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Affiliation(s)
- Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Matao Street, Travessa 14 Cidade Universitaria, São Paulo, 05508-090, São Paulo, Brazil
| | - Alfredo L Porfírio-Sousa
- Department of Zoology, Institute of Biosciences, University of São Paulo, Matao Street, Travessa 14 Cidade Universitaria, São Paulo, 05508-090, São Paulo, Brazil
| | - Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, 10 Elm Street, Northampton, Massachusetts, 01063.,Program in Organismic and Evolutionary Biology, University of Massachussetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01002-9316
| | - Laura A Katz
- Department of Biological Sciences, Smith College, 10 Elm Street, Northampton, Massachusetts, 01063
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Matao Street, Travessa 14 Cidade Universitaria, São Paulo, 05508-090, São Paulo, Brazil
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Yan Y, Maurer-Alcalá XX, Knight R, Kosakovsky Pond SL, Katz LA. Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates. mBio 2019; 10:e02524-19. [PMID: 31874915 PMCID: PMC6935857 DOI: 10.1128/mbio.02524-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022] Open
Abstract
Ciliates, a eukaryotic clade that is over 1 billion years old, are defined by division of genome function between transcriptionally inactive germline micronuclei and functional somatic macronuclei. To date, most analyses of gene family evolution have been limited to cultivable model lineages (e.g., Tetrahymena, Paramecium, Oxytricha, and Stylonychia). Here, we focus on the uncultivable Karyorelictea and its understudied sister class Heterotrichea, which represent two extremes in genome architecture. Somatic macronuclei within the Karyorelictea are described as nearly diploid, while the Heterotrichea have hyperpolyploid somatic genomes. Previous analyses indicate that genome architecture impacts ciliate gene family evolution as the most diverse and largest gene families are found in lineages with extensively processed somatic genomes (i.e., possessing thousands of gene-sized chromosomes). To further assess ciliate gene family evolution, we analyzed 43 single-cell transcriptomes from 33 ciliate species representing 10 classes. Focusing on conserved eukaryotic genes, we use estimates of transcript diversity as a proxy for the number of paralogs in gene families among four focal clades: Karyorelictea, Heterotrichea, extensive fragmenters (with gene-size somatic chromosomes), and non-extensive fragmenters (with more traditional somatic chromosomes), the latter two within the subphylum Intramacronucleata. Our results show that (i) the Karyorelictea have the lowest average transcript diversity, while Heterotrichea are highest among the four groups; (ii) proteins in Karyorelictea are under the highest functional constraints, and the patterns of selection in ciliates may reflect genome architecture; and (iii) stop codon reassignments vary among members of the Heterotrichea and Spirotrichea but are conserved in other classes.IMPORTANCE To further our understanding of genome evolution in eukaryotes, we assess the relationship between patterns of molecular evolution within gene families and variable genome structures found among ciliates. We combine single-cell transcriptomics with bioinformatic tools, focusing on understudied and uncultivable lineages selected from across the ciliate tree of life. Our analyses show that genome architecture correlates with patterns of protein evolution as lineages with more canonical somatic genomes, such as the class Karyorelictea, have more conserved patterns of molecular evolution compared to other classes. This study showcases the power of single-cell transcriptomics for investigating genome architecture and evolution in uncultivable microbial lineages and provides transcriptomic resources for further research on genome evolution.
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Affiliation(s)
- Ying Yan
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
| | - Xyrus X Maurer-Alcalá
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Rob Knight
- University of California San Diego, Department of Pediatrics, San Diego, California, USA
- University of California San Diego, Department of Computer Science and Engineering, San Diego, California, USA
- University of California San Diego, Center for Microbiome Innovation, San Diego, California, USA
| | - Sergei L Kosakovsky Pond
- Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, Pennsylvania, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
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