The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

Page, Eric; Laforest, Martin; Martin, Sara L.; Bisaillon, Katherine; Soufiane, Brahim; Meloche, Sydney; Tardif, François J.

doi:https://open-science.canada.ca/handle/123456789/2510

The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

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dc.contributor.author: Page, Eric; Laforest, Martin; Martin, Sara L.; Bisaillon, Katherine; Soufiane, Brahim; Meloche, Sydney; Tardif, François J.
dc.date.accepted: 2024-02-04
dc.date.accessioned: 2024-05-24T15:19:34Z
dc.date.available: 2024-05-24T15:19:34Z
dc.date.issued: 2024-03-13
dc.date.submitted: 2023-06-23
dc.description - en: Common and giant ragweed are important weeds with agricultural and health impacts worldwide. Here, we used a hybrid of common and giant ragweed to simultaneously produce chromosome-level assemblies of both species. These assemblies uncovered new molecular mechanisms of herbicide resistance and indicated that many of the genes believed to be responsible for the allergenicity of ragweed pollen occur in clusters of several copies. Finally, we used the genome assemblies of these and related species to reconstruct the genome of the most recent common allopolyploid ancestor.
dc.description.abstract - en: Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype—a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.
dc.description.fosrctranslation - en: L’a petite herbe à poux et la grande herbe à poux sont des mauvaises herbes importantes ayant des impacts agricoles et sanitaires dans le monde entier. Ici, nous avons utilisé un hybride de la petite ’herbe à poux et la grande herbe à poux pour produire simultanément des assemblages chromosomiques des deux espèces. Ces assemblages ont permis de découvrir de nouveaux mécanismes moléculaires de résistance aux herbicides et ont indiqué que de nombreux gènes soupçonnés d'être responsables de l'allergénicité du pollen d'ambroisie se trouvent en grappes de plusieurs copies. Enfin, nous avons utilisé les assemblages génomiques de ces espèces et d’espèces apparentées pour reconstruire le génome de l’ancêtre allopolyploïde commun le plus récent.
dc.identifier.citation: Page, E., Martin, S. L., Bisaillon, K., Soufiane, B., Meloche, S., & Tardif, F. J. (2024). The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed. The Plant Genome, e20442. https://doi.org/10.1002/tpg2.20442
dc.identifier.doi: https://doi.org/10.1002/tpg2.20442
dc.identifier.uri: https://open-science.canada.ca/handle/123456789/2510
dc.language.iso: en
dc.publisher: Crop Science Society of America
dc.rights - en: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.rights - fr: Creative Commons Attribution - Pas d'utilisation commerciale - Pas de modification 4.0 International (CC BY-NC-ND 4.0)
dc.rights.openaccesslevel - en: Green
dc.rights.openaccesslevel - fr: Vert
dc.rights.uri - en: https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.uri - fr: https://creativecommons.org/licenses/by-nc-nd/4.0/deed.fr
dc.subject - en: Nature and environment
dc.subject - fr: Nature et environnement
dc.subject.en - en: Nature and environment
dc.subject.fr - fr: Nature et environnement
dc.title - en: The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed
dc.type - en: Article
dc.type - fr: Article
local.acceptedmanuscript.articlenum: e20442
local.article.journaltitle: The Plant Genome
local.pagination: 28 pages
local.peerreview - en: Yes
local.peerreview - fr: Oui

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