Biology subjects

Patterson, E. L.

Publications and source records attributed to Patterson, E. L..

9 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↗

bioRxiv2024

A Novel Genomic Rearrangement in the Amaranthus palmeri Extrachromosomal Circular DNA Provides Dual Herbicide Resistance to Glyphosate and Glufosinate

Amplification of chloroplastic glutamine synthetase (GS2) has been characterized as one of the resistance mechanisms in glufosinate-resistant Amaranthus palmeri accession (MSR2). Previously, the overamplification of the glyphosate-resistance gene, 5-enolpyruvylshikimate-3-phosphate (EPSPS), in A. palmeri was determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, a novel eccDNA is described that carries both glyphosate and glufosinate-ammonium target site due to co-duplication of their chromosomic native region, conferring resistance. Besides EPSPS, the novel replicon has a region replaced by a fragment carrying the GS2 isoforms (GS2.1 and GS2.2) and other genes. The co-existence of eccDNA carrying only EPSPS was confirmed in MSR2 samples harboring dual targeting eccDNA. The genomic structure of GS2 and EPSPS amplification was also assessed in a different glufosinate-resistant A. palmeri accession (MSR1) along with MSR2. The accessions showed distinct GS2.1 and GS2.2 amplification patterns suggesting the existence of diverse replicons that were not assembled here. The EPSPS was amplified in both accessions, and a correlation was observed with the GS2 isoforms in MSR2, further supporting the co-existence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.

genomics↗

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

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

Duplicate transcription factors GT1 and VRS1 regulate branching and fertile flower number in maize and Brachypodium distachyon

Crop engineering and de novo domestication using genome editing are new frontiers in agriculture. However, outside of well-studied crops and model systems, prioritizing engineering targets remains challenging. Evolution can serve as our guide, revealing high-priority genes with deeply conserved roles. Indeed, GRASSY TILLERS1 (GT1), SIX-ROWED SPIKE1 (VRS1), and their homologs have repeatedly been targets of selection in domestication and evolution. This repeated selection may be because these genes have an ancient, conserved role in regulating growth repression. To test this, we determined the roles of GT1 and VRS1 homologs in maize (Zea mays) and the distantly related grass brachypodium (Brachypodium distachyon) using CRISPR-Cas9 gene editing and mutant analysis. GT1 and VRS1 have roles in floral development in maize and barley, respectively. Grass flowers are borne in branching structures called spikelets. In maize spikelets, carpels are suppressed in half of all initiated ear flowers. These spikelets can only produce single grains. We show that gt1; vrs1-like1 (vrl1) mutants have derepressed carpels in ear flowers. Importantly, these plants can produce two grains per spikelet. In brachypodium, bdgt1; bdvrl1 mutants have more branches, spikelets, and flowers than wildtype plants, indicating conserved roles for GT1 and VRS1 homologs in growth suppression. Indeed, maize GT1 can suppress growth in Arabidopsis thaliana, separated from the grasses by ca. 160 million years of evolution. Thus, GT1 and VRS1 maintain their potency as growth regulators across vast timescales and in distinct developmental contexts. Modulating the activity of these and other conserved genes may be critical in crop engineering.

plant biology↗

bioRxiv2021

Too little, too late: transcription during imbibition of lethally aged soybean seeds is weak and delayed, but not aberrant

O_TBL View this table: org.highwire.dtl.DTLVardef@116f1e7org.highwire.dtl.DTLVardef@163aa97org.highwire.dtl.DTLVardef@54d174org.highwire.dtl.DTLVardef@8342f3org.highwire.dtl.DTLVardef@1a08df1_HPS_FORMAT_FIGEXP M_TBL C_TBL O_LIThis study investigates alive to dead signals in seeds that aged during cool, dry storage. Signals may invoke abrupt, lethal metabolic pathways or reflect effects of accumulated small injuries which impair recovery from life in the dry state. C_LIO_LICohorts of soybean (Glycine max cv. Williams 82) seeds were stored for 3, 19 and 22 years. Transcriptomes of dry embryonic axes and axes 24 hours after imbibition (HAI) were sequenced to determine gene expression patterns. These cohorts showed about <2, 40, and ~99% mortality, respectively, in response to storage and aging. C_LIO_LIA total of 19,340 genes were significantly differentially expressed (SDE) in imbibed axes compared to dry axes. Gene expression patterns of imbibed axes clustered into three groups that represented high, low, and no germination potential (GP). There were 17,360 SDE genes in high-GP axes and 4,892 SDE genes, mostly upregulated, in no-GP axes. Transcriptomes of no-GP axes were similar to healthy axes at 3 HAI. C_LIO_LISlow transcription, not transcription errors or novel expression pathways, portends failure to transition from seed to seedling. We conclude that the signature of death in dry aged seeds arises from metabolism that is "too little and too late." C_LI

plant biology↗

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↗

bioRxiv2020

Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations

Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri (S) Wats. in 2006, resistant populations have been reported in 28 states. The mechanism of resistance is amplification of a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, and is unique to glyphosate-resistant plants. The replicon contains a single copy of the 10-kb 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene which causes the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. It is not known whether the resistance by this amplification mechanism evolved once and then spread across the country or evolved independently in several locations. To compare genomic representation and variation across the EPSPS replicon, whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. The high sequence conservation among GR biotypes with very few polymorphisms which were widely distributed across the USA further supports the hypothesis that glyphosate resistance most likely originated from a single population. We show that the replicon from different populations was unique to GR plants and had similar levels of amplification.

plant biology↗

bioRxiv2018

Formation of periodic pigment spots by the reaction-diffusion mechanism

Many organisms exhibit visually striking spotted or striped pigmentation patterns. Turings reaction-diffusion model postulates that such periodic pigmentation patterns form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. However, the molecular activators and repressors fully fitting this versatile model remain elusive. Here, we characterize an R2R3-MYB activator and an R3-MYB repressor in monkeyflowers that correspond to Turings model and explain how periodic anthocyanin spots form. Notably, disrupting this pattern impacts pollinator visitation. Thus, subtle changes in simple reaction-diffusion networks are likely essential contributors to the evolution of the remarkable diversity of periodic pigmentation patterns in flowers.

plant biology↗