{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/34445"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/34445","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Origin of viruses revealed by the genomic study of protein domain structures","abstract":"The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate they have evolved via massive reductive evolutionary processes. Since viral domains are widespread among cellular proteomes we propose that viruses mediate gene transfer between cellular species and crucially enhance biodiversity. Results call for a change in the way viruses are perceived. They likely represent a distinct and most ancient form of life and a very crucial part of our planet’s biosphere. Additionally, we assign functions to molecular structures in nearly a thousand proteomes and highlight the conserved nature of cellular proteomes.","abstract_html":"The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate they have evolved via massive reductive evolutionary processes. Since viral domains are widespread among cellular proteomes we propose that viruses mediate gene transfer between cellular species and crucially enhance biodiversity. Results call for a change in the way viruses are perceived. They likely represent a distinct and most ancient form of life and a very crucial part of our planet’s biosphere. Additionally, we assign functions to molecular structures in nearly a thousand proteomes and highlight the conserved nature of cellular proteomes.","abstract_has_math":false,"creators":["Nasir, Arshan"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Bioinformatics","degree_department":null,"school":null,"contributors":["Caetano-Anolles, Gustavo"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-09-18T21:17:31Z","date_published":"2012-09-18T21:17:31Z","updated_at":"2026-07-22T22:25:31Z","subjects":["Mimivurs","phylogenomics, protein domain, structure, evolution"],"languages":["en"],"rights":["Copyright 2012 Arshan Nasir. Chapter 3 copyright 2011 IEEE. In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of the University of Illinois's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/34445","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Caetano-Anolles, Gustavo"]},{"key":"dc:creator","label":"Author","values":["Nasir, Arshan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-09-18T21:17:31Z","2014-09-18T10:00:50Z","2012-08"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioinformatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Mimivurs","phylogenomics, protein domain, structure, evolution"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2012 Arshan Nasir. Chapter 3 copyright 2011 IEEE. In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of the University of Illinois's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/34445"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate they have evolved via massive reductive evolutionary processes. Since viral domains are widespread among cellular proteomes we propose that viruses mediate gene transfer between cellular species and crucially enhance biodiversity. Results call for a change in the way viruses are perceived. They likely represent a distinct and most ancient form of life and a very crucial part of our planet’s biosphere. Additionally, we assign functions to molecular structures in nearly a thousand proteomes and highlight the conserved nature of cellular proteomes.","Item withdrawn by Alexis Thompson (athmpsn1@illinois.edu) on 2012-04-26T13:29:29Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Nasir_Arshan.doc: 6206976 bytes, checksum: 760e59eee27e0c120323361e075ecf52 (MD5) Nasir_Arshan.pdf: 9769633 bytes, checksum: 28d7f8e91c2dc1cffd3fb23b515d8897 (MD5)","Made available in DSpace on 2012-09-18T21:17:31Z (GMT). No. of bitstreams: 5 Nasir_Arshan.pdf: 14343468 bytes, checksum: d05af99bbfb9595a4896ca4b40cf24db (MD5) license.txt: 4060 bytes, checksum: 8f91acb6a1c9491f976cc1c680c0b546 (MD5) Nasir_Arshan.doc: 6197248 bytes, checksum: d1fda417a851a04d211ed187c2c57c4d (MD5) 1_Nasir_Arshan.doc: 6192128 bytes, checksum: 8a3495717e559e80ce00f2f60e7a2f28 (MD5) 2_Nasir_Arshan.doc: 6207488 bytes, checksum: b5b07f771764693291b6a0203002c820 (MD5)","Restriction data tranferred 2014-07-01T11:11:20-05:00 Original Data Group with Access UIUC Users [automated] Release Date: 2014-09-18 16:21:01 UTC Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Seth Robbins (srobbins@illinois.edu) on 2012-09-18T21:21:04Z Item is restricted until 2014-09-18T21:21:01Z","U of I Only Restriction Lifted for Item 34719 on 2014-09-18T10:00:50Z."]},{"key":"dc:title","label":"Title","values":["Origin of viruses revealed by the genomic study of protein domain structures"]}]}],"canonical_facts":{"dc:contributor":["Caetano-Anolles, Gustavo"],"dc:creator":["Nasir, Arshan"],"dc:date":["2012-09-18T21:17:31Z","2014-09-18T10:00:50Z","2012-08"],"dc:description":["The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate they have evolved via massive reductive evolutionary processes. Since viral domains are widespread among cellular proteomes we propose that viruses mediate gene transfer between cellular species and crucially enhance biodiversity. Results call for a change in the way viruses are perceived. They likely represent a distinct and most ancient form of life and a very crucial part of our planet’s biosphere. Additionally, we assign functions to molecular structures in nearly a thousand proteomes and highlight the conserved nature of cellular proteomes.","Item withdrawn by Alexis Thompson (athmpsn1@illinois.edu) on 2012-04-26T13:29:29Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Nasir_Arshan.doc: 6206976 bytes, checksum: 760e59eee27e0c120323361e075ecf52 (MD5) Nasir_Arshan.pdf: 9769633 bytes, checksum: 28d7f8e91c2dc1cffd3fb23b515d8897 (MD5)","Made available in DSpace on 2012-09-18T21:17:31Z (GMT). No. of bitstreams: 5 Nasir_Arshan.pdf: 14343468 bytes, checksum: d05af99bbfb9595a4896ca4b40cf24db (MD5) license.txt: 4060 bytes, checksum: 8f91acb6a1c9491f976cc1c680c0b546 (MD5) Nasir_Arshan.doc: 6197248 bytes, checksum: d1fda417a851a04d211ed187c2c57c4d (MD5) 1_Nasir_Arshan.doc: 6192128 bytes, checksum: 8a3495717e559e80ce00f2f60e7a2f28 (MD5) 2_Nasir_Arshan.doc: 6207488 bytes, checksum: b5b07f771764693291b6a0203002c820 (MD5)","Restriction data tranferred 2014-07-01T11:11:20-05:00 Original Data Group with Access UIUC Users [automated] Release Date: 2014-09-18 16:21:01 UTC Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Seth Robbins (srobbins@illinois.edu) on 2012-09-18T21:21:04Z Item is restricted until 2014-09-18T21:21:01Z","U of I Only Restriction Lifted for Item 34719 on 2014-09-18T10:00:50Z."],"dc:identifier":["http://hdl.handle.net/2142/34445"],"dc:language":["en"],"dc:rights":["Copyright 2012 Arshan Nasir. Chapter 3 copyright 2011 IEEE. In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of the University of Illinois's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink."],"dc:subject":["Mimivurs","phylogenomics, protein domain, structure, evolution"],"dc:title":["Origin of viruses revealed by the genomic study of protein domain structures"],"thesis:degree_discipline":["Bioinformatics"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:31Z"}