Biology subjects

Gaines, T. A.

Publications and source records attributed to Gaines, T. A..

12 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

Amaranthus L. spans aggressive agricultural weeds, ornamentals, and ancient pseudocereals. Species within the genus vary in morphology, environmental tolerance, and sexual systems, making them well-suited for studying reproductive evolution and plant adaptation. To investigate sex chromosome architecture within the genus, we generated chromosome-level assemblies of a monoecious amaranth (Amaranthus spinosus) and three dioecious species (A. acanthochiton, A. arenicola, and A. floridanus) using PacBio high-fidelity (HiFi) long reads. We paired these data with Dovetail Genomics Omni-C sequencing to achieve haplotype resolution for A. spinosus and A. acanthochiton, and we used reference-guided scaffolding for the remaining two species. The assemblies are highly contiguous, with sizes ranging from 394.24 to 607.10 Mbp, contig N50 from 0.63 to 8.76 Mbp, and scaffold N50 from 22.44 to 37.97 Mbp. Evaluation of the assemblies and annotations revealed 96.3 to 97.6%, and 97.6 to 98.3% BUSCO completeness, respectively. Comparative genomic analysis revealed that the Chromosome 1 inversions and Robertsonian fusion previously reported in A. tuberculatus are conserved in A. acanthochiton and consistent with the architecture of A. arenicola and A. floridanus, suggesting that the evolution of dioecy in this clade predates subsequent speciation. In parallel, multiple homologs of Rf1 on Chromosome 3 of A. spinosus, a monoecious species that exhibits spatial separation of male and female flowers and is closely related to the dioecious A. palmeri, were identified. Together, this study provides foundational resources for advancing evolutionary, ecological, and agronomic research across the genus, including herbicide resistance evolution and weediness traits.

genomics↗

bioRxiv2025

Subgenome dominance of ALS target site mutations impacts herbicide resistance in allohexaploid Echinochloa crus-galli

Herbicide target site resistance in polyploid species is more complex than diploids due to potential subgenome interactions and gene dosage of mutations. The objective of this study was to identify the level of resistance and cross-resistance patterns of ALS mutations located in the different subgenomes of allohexaploid Echinochloa crus-galli. E. crus-galli populations were screened and dose-response curves were performed with ALS-inhibitors from different chemical groups. The ALS genes of each subgenome (A, B, and C) were sequenced. Copy number variation, global relative expression, and the specific relative expression of ALS gene from each subgenome were performed. Out of 100 populations, 32% were resistant only to imazethapyr, and 48% were cross-resistant to all ALS-inhibitors. The mutations Ala122Thr, Ala205Asn, and Ser653Asn confer resistance only to imazethapyr, while Trp574Leu confers resistance to all four herbicides tested. ALS mutations were most frequent in subgenome A, but ALS from subgenome C had the highest expression. The biotype SAOJER-01 had Trp574Leu mutation in subgenome C and was 22 times more resistant to imazethapyr and penoxsulam than CAMAQ-01, which had the same Trp574Leu mutation in subgenome A with no differences in herbicide metabolism rate. The ALS genes from subgenomes A and C contribute approximately 13% and 50% respectively to the total ALS transcripts. The higher contribution of subgenome C to the total ALS transcripts pool combined with the Trp574Leu resistance mutation makes the biotype SAOJER-01 more resistant to herbicides than CAMAQ-01. This is the first study showing the effect of subgenome gene expression level on the herbicide resistance level in a polyploid weed species. In addition, while imazethapyr did not control any biotype with an ALS mutation, the other ALS-inhibitor herbicides were able to control biotypes carrying Ala122Thr, Ala205Asn, and Ser653Asn, which reinforces the utility of these herbicides in weed and resistance management.

genetics↗

bioRxiv2025

Determination of the mechanisms of MCPA resistance in Amaranthus powellii

Resistance to 2-methyl-4-chloro-phenoxyacetic acid (MCPA) was recently confirmed in a population of green pigweed (Amaranthus powellii) from Dresden, Ontario, Canada, with a resistance factor of 4.4. Resistance to synthetic auxin herbicides in Amaranthus species has previously been linked to non-target site resistance mechanisms with low-level resistance factors (<10). Based on this information an investigation into the mechanism of resistance to MCPA was conducted in this population of green pigweed. No significant differences in absorption, translocation, and metabolism of 14C-MCPA existed between the resistant and a susceptible population of green pigweed. An RNA-Sequencing experiment to identify differentially expressed genes also confirmed this result. Genes that were differentially expressed in the resistant population were linked to target site modifications. A single nucleotide polymorphism (SNP) conferring a leucine to phenylalanine substitution was identified in auxin response factor (ARF) 9. This mutation may be in the Phox and Bem1p (PB1) domain in ARF9 which facilitates the interaction between ARFs and Aux/IAA repressor proteins. The results demonstrate that the mechanism of resistance to MCPA is not a non-target site mechanism and may be linked to a target site modification. Specifically, a SNP in ARF9 could disrupt the interaction between ARF9 and other Aux/IAAs which could prevent ubiquitination of Aux/IAAs and subsequent lethal action of MCPA.

plant biology↗

bioRxiv2024

Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region

Amaranthus palmeri (Palmer amaranth), A. retroflexus (redroot pigweed), and A. hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as pigweeds, these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. Development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweed weed species. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified a [~]2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed two genes within the male-specific region, RESTORER OF FERTILITY 1 (Rf1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.

genomics↗

bioRxiv2024

A transposable element insertion in IAA16 interrupts normal splicing and generates a novel dicamba resistance allele in Bassia scoparia

A dicamba-resistant population of kochia (Bassia scoparia) identified in Colorado, USA in 2012 was used to generate a synthetic mapping population that segregated for dicamba resistance. Linkage mapping associating dicamba injury with genotype derived from restriction-site-associated DNA sequencing identified a single locus in the kochia genome associated with resistance on chromosome 4. A mutant version of Auxin/Indole-3-Acetic Acid 16 (AUX/IAA16; a gene previously implicated in dicamba resistance in kochia) was found near the middle of this locus in resistant plants. Long read sequencing of dicamba-resistant plants identified a recently inserted Ty1/Copia retrotransposon near the beginning of the second exon of AUX/IAA16, leading to disruption of normal splicing. A molecular marker for this insertion allows for rapid detection of resistance. Stable transgenic lines of Arabidopsis thaliana ectopically expressing the mutant and wildtype alleles of AUX/IAA16 were developed. Arabidopsis thaliana plants expressing the mutant AUX/IAA16 allele grew shorter roots on control media. However, transgenic root growth was less inhibited on media containing either dicamba (5 M) or IAA (0.5 M) when compared to non-transgenic plants or those expressing the wildtype allele of AUX/IAA16. In vitro assays indicate reduced binding affinity and more rapid dissociation of the mutant AUX/IAA with TIR1 in the presence of several auxins, and protein modeling suggests the substitution of the glycine residue in the degron domain of AUX/IAA16 is especially important for resistance. A fitness cost associated with the mutant allele of AUX/IAA16 has implications for resistance evolution and management of kochia populations with this resistance mechanism. SignificanceAuxin mimics are amongst the most important herbicides in modern agriculture. Evolution of weeds that are resistant to these herbicides threatens sustainable crop production. Understanding the basis of auxin herbicide resistance informs the development of improved weed control technologies. Additionally, auxin-resistant mutations and their pleotropic effects help us understand auxin perception and signalling. We describe a transposable element insertion within an herbicide target site gene that alters splicing and reduces synthetic and natural auxin perception.

plant biology↗

bioRxiv2024

A phased chromosome-level genome assembly provides insights into the evolution of sex chromosomes in Amaranthus tuberculatus

O_LIAmaranthus tuberculatus (waterhemp) is a troublesome weed species of agronomic importance that is dioecious with an XY sex-determination system. The evolution of sex chromosomes, the contiguity of sex-determining region (SDR) and the expression pattern of genes within the SDR remain poorly understood. C_LIO_LIWe assembled the genome of a male A. tuberculatus, phased the genome into two chromosome-level haplotypes, and performed restriction site-associated DNA genome- wide association (RAD-GWA) analysis, comparative genomics, adaptive evolution analysis, and, with existing data, transcriptomic profiling to characterize the species sex chromosomes. C_LIO_LIComparative analysis enabled the identification of a [~]32.8 Mb SDR on chromosome 1 that is gene-poor, abundant in long terminal repeat (LTR) retrotransposons, and harbors two inversions. Synteny analysis revealed that chromosome 1 likely originated from the fusion of two ancestral chromosomes, and mRNA data indicated 93 genes out of the 531 protein-coding genes within the SDR of haplome 2 were differentially expressed between mature male and female flowers, with several of the genes enriched for Gene Ontology (GO) terms involved in floral development. C_LIO_LIBeyond adding to our understanding of sex chromosome evolution, the genomic resource provided here will be valuable for addressing further questions on adaptive trait evolution in Amaranthus. C_LI

genomics↗

bioRxiv2023

CYTOCHROME P450 CYP72A219 IS INVOLVED IN EVOLUTION OF METABOLIC RESISTANCE TO TEMBOTRIONE IN Amaranthus palmeri POPULATIONS

Evolution of metabolic herbicide resistance is a major issue for weed management. Few genes and regulatory mechanisms have been identified, particularly in dicotyledonous weed species. We identified putative causal genes and regulatory mechanism for tembotrione-resistance in Amaranthus palmeri. Cytochrome P450 candidate genes were identified through RNA-seq analysis. We validated their functions using heterologous expression in S. cerevisae. Promoters of the candidate P450 genes were analyzed. We performed QTL mapping to identify genomic regions associated with resistance. CYP72A1182 deactivated tembotrione. This gene had increased expression in other A. palmeri populations resistant to multiple herbicides, including tembotrione. Resistant plants exhibited polymorphisms in the promoter of CYP72A1182. We identified QTLs linked to herbicide resistance, including one on chromosome 4 approximately 3 Mb away from CYP72A1182. CYP72A1182 is involved in tembotrione resistance in A. palmeri. Increased expression of this gene could be due to cis-regulation in the promoter, as well as trans-regulation from transcription factors. Further studies are in progress to test this hypothesis. The elucidation of regulatory genes is crucial for developing innovative weed management approaches and target-based novel molecules. HIGHLIGHTSOur study identifies that the CYP72A1182 gene has a functional role in metabolic herbicide resistance in Amaranthus palmeri and is linked to cis-regulatory polymorphisms, advancing metabolic resistance understanding in dicots.

plant biology↗

bioRxiv2023

Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

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 an agronomically problematic Great Plains tumbleweed, kochia (Bassia scoparia). A 2014 field survey for herbicide resistance in kochia populations across Colorado identified a putative fluroxypyr resistant population that was assessed for response to five different herbicides representing four different herbicide modes of action. These included fluroxypyr and dicamba (auxin-mimics), atrazine (photosystem II inhibitor), glyphosate (EPSPS inhibitor), and chlorsulfuron (acetolactate synthase inhibitor). The greenhouse screen identified that this kochia population was resistant to fluroxypyr and chlorsulfuron, but sensitive to glyphosate, atrazine, and dicamba. This population was designated Flur-R. Subsequent dose response studies determined that 75% of the Flur-R population survived 628 g ae ha-1 of fluroxypyr (4X the label application rate in wheat fallow, which is 157 g ae ha-1 at 1X). 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 9425 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. Formation and flux of these metabolites was 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. Significance StatementHerbicide resistance is an ever-present issue in weeds of cropping and rangeland systems. By understanding genetic mechanisms of resistance in individual cases of herbicide resistance, we can extrapolate important information such as how quickly resistance to a specific herbicide can spread. Every characterized herbicide resistance mechanism contributes to a working database used to address herbicide resistance in an agricultural or open-space setting. Knowing the exact mechanism of resistance helps researchers and industry members understand why herbicide applications are failing, and if resistant plants can still be controlled with other herbicide modes of action. In kochia line Flur-R, there is strong evidence to support a non-target site resistance mechanism, specifically herbicide degradation via increased enzymatic activity. Increased fluroxypyr degradation represents a novel resistance mechanism to fluroxypyr in the weed Bassia scoparia.

plant biology↗

bioRxiv2023

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

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2023

FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome

A near complete genome assembly consisting of 14 scaffolds, a total length of 969.6 Mb, and N50 scaffold length of 99.88 Mb, was generated to better understand how transposable element activity has led to adaptive evolution in Bassia scoparia (kochia), an agronomically important weed. The 9 largest scaffolds correspond to the 9 chromosomes of the close relative, Beta vulgaris. From this assembly, 54,387 protein-coding gene loci were annotated. We determined that genes containing Far-Red Elongated Hypocotyl 3 (FHY3) or Far-Red Impaired Response 1 (FAR1) functional domains have undergone a large, kochia-specific gene family expansion. We discovered that putative Mutator Don-Robertson (MuDR) transposable elements with detectable FHY3/FAR1 domains were tightly associated with segmental duplications of 5-enolpyruvylshikimate-3-phosphate synthase subsequently conferring resistance to the herbicide glyphosate. Further, we characterized a new MuDR subtype, named here as "Muntjac", which contributes to the evolution of herbicide resistance in kochia through the process of transduplication. Collectively, our study provides insights into the role of a FHY3/FAR1 gene as an active transposable element and contributes new perspectives on the interaction between transposons and herbicide resistance evolution. Significance StatementIn this work we discover that genes known as FHY3/FAR1, supposed "domesticated transposons", are still actively transposing in the weed Bassia scoparia rearranging the genome in new ways. One rearrangement they are involved in is the tandem duplication of the gene 5-enolpyruvylshikimate-3-phosphate synthase which is the gene that produces the target protein of glyphosate, one of the most important herbicides in the world. This work gives a specific example of the role that transposable elements play in making novel genetics and therefore the role that new genome rearrangements play in adaptative evolution, especially in response to external stress such as herbicides.

genomics↗

bioRxiv2021

An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale

The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides mimic the effects of IAA by inducing strong auxinic signaling responses in plants. Synthetic auxins are crucial herbicides in agriculture, made more important by the recent introduction of transgenic synthetic auxin resistant soybean and cotton. Currently, 41 weed species have evolved resistance to synthetic auxin herbicides and, in all but one case, the molecular basis of these resistance mechanisms is unknown. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and-susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing 9 amino acids in the degron tail (DT) of the auxin co-receptor Aux/IAA2 (SoIAA2). The deletion allele co-segregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This novel mechanism of synthetic auxin herbicide resistance assigns a new in planta function to the DT region of this Aux/IAA co-receptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin resistant crops using gene editing.

plant biology↗

bioRxiv2019

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the worlds most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing a kochia bacterial artificial chromosome library. These resources helped reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are co-duplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. We discovered a FHY3/FAR1-like mobile genetic element that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.

genomics↗