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dc.creatorde Klerk, Arne
dc.creatorSwanepoel, Phillip
dc.creatorLourens, Rentia
dc.creatorZondo, Mpumelelo
dc.creatorAbodunran, Isaac
dc.creatorLytras, Spyros
dc.creatorMacLean, Oscar A.
dc.creatorRobertson, David
dc.creatorPond, Sergei
dc.creatorZehr, Jordan
dc.creatorKumar, Venkatesh
dc.creatorStanhope, Michael J.
dc.creatorHarkins, Gordon W.
dc.creatorMurrell, Ben
dc.creatorMartin, Darren P.
dc.date.accessioned2022-08-29T17:20:38Z
dc.date.available2022-08-29T17:20:38Z
dc.date.issued2022-06-14
dc.identifier.citationArné de Klerk, Phillip Swanepoel, Rentia Lourens, Mpumelelo Zondo, Isaac Abodunran, Spyros Lytras, Oscar A MacLean, David Robertson, Sergei L Kosakovsky Pond, Jordan D Zehr, Venkatesh Kumar, Michael J Stanhope, Gordon Harkins, Ben Murrell, Darren P Martin, Conserved recombination patterns across coronavirus subgenera, Virus Evolution, Volume 8, Issue 2, 2022, veac054, https://doi.org/10.1093/ve/veac054
dc.identifier.issn2057-1577
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/8053
dc.identifier.urihttp://hdl.handle.net/20.500.12613/8081
dc.description.abstractRecombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination break points at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns. Specifically, we confirm the non-randomness of recombination break points across all six tested coronavirus subgenera, locate conserved recombination hot- and cold-spots, and determine that the locations of transcriptional regulatory sequences are likely major determinants of conserved recombination break-point hotspot locations. We find that while the locations of recombination break points are not uniformly associated with degrees of nucleotide sequence conservation, they display significant tendencies in multiple coronavirus subgenera to occur in low guanine-cytosine content genome regions, in non-coding regions, at the edges of genes, and at sites within the Spike gene that are predicted to be minimally disruptive of Spike protein folding. While it is apparent that sequence features such as transcriptional regulatory sequences are likely major determinants of where the template-switching events that yield recombination break points most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination break-point distributions in coronavirus genomes sampled from nature.
dc.format.extent15 pages
dc.languageEnglish
dc.language.isoeng
dc.relation.ispartofCOVID-19 Research
dc.relation.haspartVirus Evolution, Vol. 8, No. 2
dc.relation.isreferencedbyOxford University Press
dc.rightsAttribution-NonCommercial CC BY-NC
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectCoronavirus
dc.subjectPhylogenetics
dc.subjectEvolution
dc.subjectRecombination
dc.subjectSelection
dc.titleConserved recombination patterns across coronavirus subgenera
dc.typeText
dc.type.genreJournal article
dc.contributor.groupInstitute for Genomics and Evolutionary Medicine (Temple University)
dc.description.departmentBiology
dc.relation.doihttps://doi.org/10.1093/ve/veac054
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.description.schoolcollegeTemple University. College of Science and Technology
dc.creator.orcidPond|0000-0003-4817-4029
dc.creator.orcidZehr|0000-0003-2099-4172
dc.temple.creatorKosakovsky Pond, Sergei L.
dc.temple.creatorZehr, Jordan D.
refterms.dateFOA2022-08-29T17:20:38Z


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