{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:31:21Z","timestamp":1785421881520,"version":"3.56.0"},"reference-count":54,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T00:00:00Z","timestamp":1750809600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T00:00:00Z","timestamp":1750809600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSphere"],"published-print":{"date-parts":[[2025,6,25]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      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 well documented among non-model ciliates, including\n                      <jats:italic toggle=\"yes\">Chilodonella uncinata<\/jats:italic>\n                      (class Phyllopharyngea), the focus of our work. Here, we characterize nuclear architecture and genome dynamics in\n                      <jats:italic toggle=\"yes\">C. uncinata<\/jats:italic>\n                      by combining 4\u2032,6-diamidino-2-phenylindole (DAPI) staining and fluorescence\n                      <jats:italic toggle=\"yes\">in situ<\/jats:italic>\n                      hybridization (FISH) techniques with confocal microscopy. We developed a telomere probe for staining, which alongside DAPI allows for the identification of fragmented somatic chromosomes among the total DNA in the nuclei. We quantify both total DNA and telomere-bound signals from more than 250 nuclei sampled from 116 individual cells, and analyze changes in DNA content and nuclear architecture across\n                      <jats:italic toggle=\"yes\">Chilodonella<\/jats:italic>\n                      \u2019s nuclear life cycle. Specifically, we find that MAC developmental stages in the ciliate\n                      <jats:italic toggle=\"yes\">C. uncinata<\/jats:italic>\n                      are different from those reported from other ciliate species. These data provide insights into nuclear dynamics during development and enrich our understanding of genome evolution in non-model ciliates.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Ciliates are a clade of diverse single-celled eukaryotic microorganisms that contain at least one somatic macronucleus (MAC) and germline micronucleus (MIC) within each cell\/organism. Ciliates rely on complex genome rearrangements to generate somatic genomes from a zygotic nucleus. However, the development of somatic nuclei has only been documented for a few model ciliate genera, including\n                      <jats:italic toggle=\"yes\">Paramecium<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Tetrahymena<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Oxytricha<\/jats:italic>\n                      . Here, we study the MAC developmental process in the non-model ciliate,\n                      <jats:italic toggle=\"yes\">C. uncinata<\/jats:italic>\n                      . We analyze both total DNA and the generation of gene-sized somatic chromosomes using a laser scanning confocal microscope to describe\n                      <jats:italic toggle=\"yes\">C. uncinata<\/jats:italic>\n                      \u2019s nuclear life cycle. We show that DNA content changes dramatically during their life cycle and in a manner that differs from previous studies on model ciliates. Our study expands knowledge of genome dynamics in ciliates and among eukaryotes more broadly.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00075-25","type":"journal-article","created":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T09:00:31Z","timestamp":1746781231000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Genome content reorganization in the non-model ciliate\n                    <i>Chilodonella uncinata<\/i>\n                    : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4550-9575","authenticated-orcid":false,"given":"Ragib","family":"Ahsan","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0072zz521","id-type":"ROR","asserted-by":"publisher"}],"name":"Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst","place":["Amherst, USA"]},{"id":[{"id":"https:\/\/ror.org\/0497crr92","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, Smith College","place":["Northampton, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7499-9369","authenticated-orcid":false,"given":"Xyrus X.","family":"Maurer-Alcal\u00e1","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03thb3e06","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9138-4702","authenticated-orcid":true,"given":"Laura A.","family":"Katz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0072zz521","id-type":"ROR","asserted-by":"publisher"}],"name":"Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst","place":["Amherst, USA"]},{"id":[{"id":"https:\/\/ror.org\/0497crr92","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, Smith College","place":["Northampton, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1007\/s13238-015-0147-3"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-cellbio-120420-020656"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1110633108"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0959-437x(00)00137-4"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/jeu.12898"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-020-03555-2"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/mmbr.00184-22"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a017764"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2009.05.007"},{"key":"e_1_3_4_11_2","first-page":"151","article-title":"Structure and genetic organization of the polyploid macronucleus of ciliates: a comparative review","volume":"34","author":"Raikov IB","year":"1995","unstructured":"Raikov IB. 1995. 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