{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T06:57:42Z","timestamp":1790146662310,"version":"4.0.1"},"reference-count":112,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,2,2]],"date-time":"2021-02-02T00:00:00Z","timestamp":1612224000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["P305\/11\/1061"],"award-info":[{"award-number":["P305\/11\/1061"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["16-06123S"],"award-info":[{"award-number":["16-06123S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre for research of pathogenicity and virulence of parasites","award":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000759"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000759"]}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Microbial Communities in Biomedical and Environmental Areas"},{"name":"EU H2020","award":["810224"],"award-info":[{"award-number":["810224"]}]},{"name":"University Research Centre","award":["SCI\/12"],"award-info":[{"award-number":["SCI\/12"]}]},{"name":"Ministry of Education, Youh, and Sport","award":["LM2018131"],"award-info":[{"award-number":["LM2018131"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host\u2013parasite interactions. In contrast, gene gains identified in the M.\u00a0balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).<\/jats:p>","DOI":"10.1093\/molbev\/msab020","type":"journal-article","created":{"date-parts":[[2021,1,22]],"date-time":"2021-01-22T23:14:36Z","timestamp":1611357276000},"page":"2240-2259","source":"Crossref","is-referenced-by-count":24,"title":["The <i>Mastigamoeba balamuthi<\/i> Genome and the Nature of the Free-Living Ancestor of <i>Entamoeba<\/i>"],"prefix":"10.1093","volume":"38","author":[{"given":"Vojt\u011bch","family":"\u017d\u00e1rsk\u00fd","sequence":"first","affiliation":[{"name":"Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladim\u00edr","family":"Klime\u0161","sequence":"additional","affiliation":[{"name":"Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Pa\u010des","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u010cestm\u00edr","family":"Vl\u010dek","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milu\u0161e","family":"Hradilov\u00e1","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladim\u00edr","family":"Bene\u0161","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"N\u00fdvltov\u00e1","sequence":"additional","affiliation":[{"name":"Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Hrd\u00fd","sequence":"additional","affiliation":[{"name":"Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Pyrih","sequence":"additional","affiliation":[{"name":"Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Mach","sequence":"additional","affiliation":[{"name":"Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lael","family":"Barlow","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney W","family":"Stairs","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada"},{"name":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Eme","sequence":"additional","affiliation":[{"name":"Diversity, Ecology and Evolution of Microbes (DEEM), Unit\u00e9 Ecologie Syst\u00e9matique Evolution Universit\u00e9 Paris-Saclay, Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil","family":"Hall","sequence":"additional","affiliation":[{"name":"The Earlham Institute, Norwich Research Park, Norwich, United Kingdom"},{"name":"School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Eli\u00e1\u0161","sequence":"additional","affiliation":[{"name":"Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel B","family":"Dacks","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada"},{"name":"Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada"},{"name":"Institute of Parasitology, Biology Centre, CAS, v.v.i., Ceske Budejovice, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Roger","sequence":"additional","affiliation":[{"name":"Department of Biochemistry 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