{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T11:43:00Z","timestamp":1777635780767,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,24]],"date-time":"2019-01-24T00:00:00Z","timestamp":1548288000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABI-1551363"],"award-info":[{"award-number":["ABI-1551363"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABI-1458359"],"award-info":[{"award-number":["ABI-1458359"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["National Science Foundation"],"award-info":[{"award-number":["National Science Foundation"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ECC-1617626"],"award-info":[{"award-number":["ECC-1617626"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets of components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-ATPase, the ribosome, or the flagellar motor: each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are classic examples of a complex system. An operon\u2019s genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operon\u2019s gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software accompanying this paper is available under GPLv3 license on: https:\/\/github.com\/nguyenngochuy91\/Ancestral-Blocks-Reconstruction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz053","type":"journal-article","created":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T15:21:36Z","timestamp":1548084096000},"page":"2998-3004","source":"Crossref","is-referenced-by-count":10,"title":["Tracing the ancestry of operons in bacteria"],"prefix":"10.1093","volume":"35","author":[{"given":"Huy N","family":"Nguyen","sequence":"first","affiliation":[{"name":"lowa State University Department of Veterinary Microbiology and Preventive Medicine, , Ames, IA, USA"},{"name":"Iowa State University Department of Computer Science, , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8190-2978","authenticated-orcid":false,"given":"Ashish","family":"Jain","sequence":"additional","affiliation":[{"name":"Iowa State University Department of Genetics, Development, and Cell Biology, , Ames, IA, USA"},{"name":"Iowa State University Program in Bioinformatics and Computational Biology, , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oliver","family":"Eulenstein","sequence":"additional","affiliation":[{"name":"Iowa State University Department of Computer Science, , Ames, IA, USA"},{"name":"Iowa State University Program in Bioinformatics and Computational Biology, , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1789-8000","authenticated-orcid":false,"given":"Iddo","family":"Friedberg","sequence":"additional","affiliation":[{"name":"lowa State University Department of Veterinary Microbiology and Preventive Medicine, , Ames, IA, USA"},{"name":"Iowa State University Program in Bioinformatics and Computational Biology, , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,1,24]]},"reference":[{"key":"2023062803480429700_btz053-B1","author":"Acharya","year":"2009"},{"key":"2023062803480429700_btz053-B2","doi-asserted-by":"crossref","first-page":"4463","DOI":"10.1073\/pnas.97.9.4463","article-title":"Evolution of biological complexity","volume":"97","author":"Adami","year":"2000","journal-title":"Proc. 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