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dc.contributor.authorHao, Y.
dc.contributor.authorMabry, M.E.
dc.contributor.authorEdger, P.P.
dc.contributor.authorFreeling, M.
dc.contributor.authorZheng, C.
dc.contributor.authorJin, L.
dc.contributor.authorVanBuren, R.
dc.contributor.authorColle, M.
dc.contributor.authorAn, H.
dc.contributor.authorAbrahams, R.S.
dc.contributor.authorWashburn, J.D.
dc.contributor.authorQi, X.
dc.contributor.authorBarry, K.
dc.contributor.authorDaum, C.
dc.contributor.authorShu, S.
dc.contributor.authorSchmutz, J.
dc.contributor.authorSankoff, D.
dc.contributor.authorBarker, M.S.
dc.contributor.authorLyons, E.
dc.contributor.authorPires, J.C.
dc.contributor.authorConant, G.C.
dc.date.accessioned2021-07-17T02:53:29Z
dc.date.available2021-07-17T02:53:29Z
dc.date.issued2021
dc.identifier.citationHao, Y., Mabry, M. E., Edger, P. P., Freeling, M., Zheng, C., Jin, L., VanBuren, R., Colle, M., An, H., Abrahams, R. S., Washburn, J. D., Qi, X., Barry, K., Daum, C., Shu, S., Schmutz, J., Sankoff, D., Barker, M. S., Lyons, E., … Conant, G. C. (2021). The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible. Genome Research, 31(5), 799–810.
dc.identifier.issn1088-9051
dc.identifier.pmid33863805
dc.identifier.doi10.1101/GR.270033.120
dc.identifier.urihttp://hdl.handle.net/10150/660752
dc.description.abstractThe members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: The individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match"model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty. © 2021 Hao et al.
dc.language.isoen
dc.publisherCold Spring Harbor Laboratory Press
dc.rights© 2021 Hao et al. Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleThe contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible
dc.typeArticle
dc.typetext
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, University of Arizona
dc.contributor.departmentBIO5 Institute, University of Arizona
dc.identifier.journalGenome Research
dc.description.noteOpen acess article
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
dc.eprint.versionFinal published version
dc.source.journaltitleGenome Research
refterms.dateFOA2021-07-17T02:53:29Z


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© 2021 Hao et al. Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
Except where otherwise noted, this item's license is described as © 2021 Hao et al. Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.