The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

Montgomery, Jacob S.; Morran, Sarah; MacGregor, Dana R.; McElroy, J. Scott; Neve, Paul; Neto, Célia; Vila‐Aiub, Martin M.; Sandoval, Marco; Menéndez, Analía I.; Kreiner, Julia M.; Fan, Longjiang; Caicedo, Ana L.; Maughan, Peter J.; Martins, Bianca Assis Barbosa; Mika, J.; Collavo, Alberto; Merotto, Aldo; Subramanian, Nithya; Bagavathiannan, Muthukumar; Cutti, Luan; Mazharul, Islam Md; Gill, Bikram S.; Cicchillo, Robert M.; Gast, Roger E.; Soni, Neeta; Wright, Terry R.; Zastrow-Hayes, Gina; May, Gregory D.; Malone, Jenna; Sehgal, Deepmala; Kaundun, Shiv Shankhar; Dale, Richard P.; Vorster, Juan; Peters, B.; Lerchl, Jens; Tranel, Patrick J.; Beffa, Roland; Jugulam, Mithila; Fengler, Kevin; Llaca, Víctor; Patterson, Eric; Gaines, Todd A.

doi:10.1101/2023.07.19.549613

Cited by 8 publications

(8 citation statements)

References 197 publications

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“…Six additional species are currently sequenced by large sequencing initiatives (Darwin Tree of Life project 13 , i5k 23 , Aqua-FAANG 24 , the International Weed Genome Consortium 25 ) likely resulting in high quality genomes which were not considered in the current analysis (see ESM Table S3). We found that both the available and high-quality genomic resources have unequal coverage among the large taxonomic groupings with vertebrates having the highest total number and percent coverage, followed by plants and invertebrates (Table1).…”

Section: Resultsmentioning

confidence: 99%

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Missing genomic resources for the next generation of environmental risk assessment

Roell,

Ott,

Mair

et al. 2023

Preprint

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Environmental risk assessment traditionally relies on a wide range of in vivo testing to assess the potential hazard of chemicals in the environment. These tests are often time-consuming, costly and can cause test organism suffering. Recent developments of reliable low-cost alternatives, both in vivo- and in silico-based, opened the door to reconsider current toxicity assessment. However, many of these new approach methodologies (NAMs) rely on high quality annotated genomes for surrogate species of the regulatory risk assessment. Currently, lacking genomic information slows the process of NAM development. Here, we present a phylogenetically resolved overview of missing genomic resources for surrogate species within regulatory ecotoxicological risk assessment. We call for an organized and systematic effort within the (regulatory) ecotoxicological community to provide these missing genomic resources. Further, we discuss the potential of a standardized genomic surrogate species landscape to enable a robust and non-animal reliant ecotoxicological risk assessment in the systems ecotoxicology era.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Missing genomic resources for the next generation of environmental risk assessment

Roell,

Ott,

Mair

et al. 2023

Preprint

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“…Metabolite identification via LCMS/MS is a crucial next step to determine the metabolic path of the fluroxypyr molecule. Other future studies include genetic mapping of fluroxypyr resistance via test crosses and either Quantitative Trait Loci (QTL) or bulk‐segregant analysis with resistant Flur‐R and susceptible J01‐S, which will provide chromosomal location of resistance gene(s) (Montgomery et al, 2023). Biochemical studies using P450 and GST inhibitors will indicate whether the enhanced fluroxypyr metabolism can be reversed.…”

Section: Future Workmentioning

confidence: 99%

Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

Todd,

Patterson,

Westra

et al. 2024

Plant Direct

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Auxin‐mimic herbicides chemically mimic the phytohormone indole‐3‐acetic‐acid (IAA). Within the auxin‐mimic herbicide class, the herbicide fluroxypyr has been extensively used to control kochia (Bassia scoparia). A 2014 field survey for herbicide resistance in kochia populations across Colorado identified a putative fluroxypyr‐resistant (Flur‐R) population that was assessed for response to fluroxypyr and dicamba (auxin‐mimics), atrazine (photosystem II inhibitor), glyphosate (EPSPS inhibitor), and chlorsulfuron (acetolactate synthase inhibitor). This population was resistant to fluroxypyr and chlorsulfuron but sensitive to glyphosate, atrazine, and dicamba. Subsequent dose‐response studies determined that Flur‐R was 40 times more resistant to fluroxypyr than a susceptible population (J01‐S) collected from the same field survey (LD50 720 and 20 g ae ha−1, respectively). Auxin‐responsive gene expression increased following fluroxypyr treatment in Flur‐R, J01‐S, and in a dicamba‐resistant, fluroxypyr‐susceptible line 9,425 in an RNA‐sequencing experiment. In Flur‐R, several transcripts with molecular functions for conjugation and transport were constitutively higher expressed, such as glutathione S‐transferases (GSTs), UDP‐glucosyl transferase (GT), and ATP binding cassette transporters (ABC transporters). After analyzing metabolic profiles over time, both Flur‐R and J01‐S rapidly converted [14C]‐fluroxypyr ester, the herbicide formulation applied to plants, to [14C]‐fluroxypyr acid, the biologically active form of the herbicide, and three unknown metabolites. The formation and flux of these metabolites were faster in Flur‐R than J01‐S, reducing the concentration of phytotoxic fluroxypyr acid. One unique metabolite was present in Flur‐R that was not present in the J01‐S metabolic profile. Gene sequence variant analysis specifically for auxin receptor and signaling proteins revealed the absence of non‐synonymous mutations affecting auxin signaling and binding in candidate auxin target site genes, further supporting our hypothesis that non‐target site metabolic degradation is contributing to fluroxypyr resistance in Flur‐R.

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“…Recent reference genomes are now routinely assembled accompanied by HI‐C, facilitating the identification of distal regulatory elements 60 . This approach is being used by the International Weeds Genomics Consortium to assemble the reference genomes from multiple weed species 61 …”

Section: Approaches For Identification Of Regulatory Elements and Cro...mentioning

confidence: 99%

“…60 This approach is being used by the International Weeds Genomics Consortium to assemble the reference genomes from multiple weed species. 61 These approaches have been applied to build cistromes and to characterize chromatin states during different physiological stages and stresses. For example, the cistrome was built for Arabidopsis, where 1812 TFs and their binding sites were characterized.…”

Section: Discovery and Characterization Of Regulatory Elementsmentioning

confidence: 99%

Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance

Bobadilla,

Tranel

2023

Pest Management Science

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The emergence of herbicide‐resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern due to its unpredictability. Nontarget‐site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC‐seq and DAP‐seq to identify transcription factors and cis‐regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds.This article is protected by copyright. All rights reserved.

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The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

Cited by 8 publications

References 197 publications

Missing genomic resources for the next generation of environmental risk assessment

Missing genomic resources for the next generation of environmental risk assessment

Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance

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