Nuclear dualism without extensive DNA elimination in the ciliate Loxodes magnus
Edited by Michael Lynch, Arizona State University, Tempe, AZ; received January 17, 2024; accepted August 8, 2024
Significance
Developmental genome editing exemplifies the evolution of biological complexity: Why do some eukaryotes carry extra genetic material that is excised in a complicated, costly, and time-consuming manner following sex? Ciliates are among the best-studied models of this phenomenon, however, this study reports a species where extensive editing could not be detected, but which nonetheless maintains substantial differences in DNA modifications and chromatin between its actively transcribed somatic nuclei and silent germline nuclei. This demonstrates that extensive genome editing is not a prerequisite for ciliate nuclear functional differentiation, and challenges the conventional theories about editing: that it is necessary as defense against mobile elements, and that editing, once gained, cannot be lost because of an evolutionary ratchet.
Abstract
Most eukaryotes have one nucleus and nuclear genome per cell. Ciliates have instead evolved distinct nuclei that coexist in each cell: a silent germline vs. transcriptionally active somatic nuclei. In the best-studied model species, both nuclei can divide asexually, but only germline nuclei undergo meiosis and karyogamy during sex. Thereafter, thousands of DNA segments, called internally eliminated sequences (IESs), are excised from copies of the germline genomes to produce the streamlined somatic genome. In Loxodes, however, somatic nuclei cannot divide but instead develop from germline copies even during asexual cell division, which would incur a huge overhead cost if genome editing was required. Here, we purified and sequenced both genomes in Loxodes magnus to see whether their nondividing somatic nuclei are associated with differences in genome architecture. Unlike in other ciliates studied to date, we did not find canonical germline-limited IESs, implying Loxodes does not extensively edit its genomes. Instead, both genomes appear large and equivalent, replete with retrotransposons and repetitive sequences, unlike the compact, gene-rich somatic genomes of other ciliates. Two other hallmarks of nuclear development in ciliates—domesticated DDE-family transposases and editing-associated small RNAs—were also not found. Thus, among the ciliates, Loxodes genomes most resemble those of conventional eukaryotes. Nonetheless, base modifications, histone marks, and nucleosome positioning of vegetative Loxodes nuclei are consistent with functional differentiation between actively transcribed somatic vs. inactive germline nuclei. Given their phylogenetic position, it is likely that editing was present in the ancestral ciliate but secondarily lost in the Loxodes lineage.
Data, Materials, and Software Availability
Software is archived on Zenodo (49, 84–86, 94, 96, 105, 113–115, 122). Sequencing data are deposited in the European Nucleotide Archive (ENA) (81, 83, 87, 100). Flow cytometry data (123–127), Western blots (128), immunofluorescence imaging (129), L. magnus genome annotations (82), and variant calling (130) are deposited in EDMOND (Max Planck Digital Library).
Acknowledgments
We thank Insa Hirschberg and Frank Chan for training and access to the BD FACSMelody; the Max Planck Genome Centre Cologne (https://mpgc.mpipz.mpg.de/home/) for PacBio and RNA-seq library preparation and sequencing; Heike Budde, Christa Lanz, and the Max Planck Institute for Biology Genome Center for additional sequencing; Andre Noll for computer system administration; Abigail Howell and Michael Borg for suggestions on flow sorting; Aurora Panzera, Vanessa Carlos, and Christian Feldhaus for assistance with optical microscopy; Jürgen Berger and Iris Koch for electron microscopy; Sinja Mattes and Amelie Albrecht for culture maintenance; and Klaus Eisler for gift of strains from the former Tübingen teaching collection. This research was supported by the Max-Planck-Gesellschaft.
Author contributions
B.K.B.S., A.S., and E.S. designed research; B.K.B.S., A.S., C.E., and E.S. performed research; D.E.V., M.P., V.S., and B.H. contributed new reagents/analytic tools; B.K.B.S., A.S., D.E.V., and E.S. analyzed data; and B.K.B.S., A.S., D.E.V., C.E., M.P., V.S., and E.S. wrote the paper.
Competing interests
The authors declare no competing interest.
Supporting Information
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B. K. B. Seah, C. Emmerich, A. Singh, E. Swart, “Immunofluorescence of Loxodes ciliate nuclei for histones, histone marks and 6mA.” Edmond. Available at https://doi.org/10.17617/3.VWAUYE. Deposited 24 June 2023.
130
B. K. B. Seah, E. Swart, “Loxodes magnus indel polymorphisms and variant calling.” Edmond. Available at https://doi.org/10.17617/3.NEV8C1. Deposited 29 July 2023.
Information & Authors
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Cover image: Pictured are rescue tigers (Panthera tigris) at In-Sync Exotics Wildlife Rescue and Educational Center in Wylie, Texas. Ellie Armstrong, Jazlyn Mooney et al. explored the genomic diversity of the privately owned captive tiger population in the United States based on genomic sequencing of 138 individuals. The study population had ancestry from all six extant wild tiger subspecies and measures of genetic diversity and inbreeding that were comparable to wild tiger populations. The results could help inform tiger conservation efforts and illegal trafficking investigations. See the article by Armstrong, Mooney et al. e2402924121. Image credit: Keri Ostermann (In-Sync Exotics Wildlife Rescue and Educational Center, Wylie, TX).
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Copyright
Copyright © 2024 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).
Data, Materials, and Software Availability
Software is archived on Zenodo (49, 84–86, 94, 96, 105, 113–115, 122). Sequencing data are deposited in the European Nucleotide Archive (ENA) (81, 83, 87, 100). Flow cytometry data (123–127), Western blots (128), immunofluorescence imaging (129), L. magnus genome annotations (82), and variant calling (130) are deposited in EDMOND (Max Planck Digital Library).
Submission history
Received: January 17, 2024
Accepted: August 8, 2024
Published online: September 19, 2024
Published in issue: September 24, 2024
Keywords
Acknowledgments
We thank Insa Hirschberg and Frank Chan for training and access to the BD FACSMelody; the Max Planck Genome Centre Cologne (https://mpgc.mpipz.mpg.de/home/) for PacBio and RNA-seq library preparation and sequencing; Heike Budde, Christa Lanz, and the Max Planck Institute for Biology Genome Center for additional sequencing; Andre Noll for computer system administration; Abigail Howell and Michael Borg for suggestions on flow sorting; Aurora Panzera, Vanessa Carlos, and Christian Feldhaus for assistance with optical microscopy; Jürgen Berger and Iris Koch for electron microscopy; Sinja Mattes and Amelie Albrecht for culture maintenance; and Klaus Eisler for gift of strains from the former Tübingen teaching collection. This research was supported by the Max-Planck-Gesellschaft.
Author Contributions
B.K.B.S., A.S., and E.S. designed research; B.K.B.S., A.S., C.E., and E.S. performed research; D.E.V., M.P., V.S., and B.H. contributed new reagents/analytic tools; B.K.B.S., A.S., D.E.V., and E.S. analyzed data; and B.K.B.S., A.S., D.E.V., C.E., M.P., V.S., and E.S. wrote the paper.
Competing Interests
The authors declare no competing interest.
Notes
Preprint server: bioRxiv, https://doi.org/10.1101/2023.11.09.566212, CC-BY 4.0 International License.
This article is a PNAS Direct Submission.
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