Chromosome-scale genome assembly ofPoa trivialisand population genomics reveals widespread gene flow in a cool-season grass seed production system DOI Creative Commons
Caio A. C. G. Brunharo, Christopher W. Benson, David R. Huff

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 5, 2023

Abstract Poa trivialis (L.) is a cool-season grass species found in various environments worldwide. In addition to being desired turfgrass species, it common weed of agricultural systems and natural areas. As weed, an important contaminant commercial seed lots, resulting widespread gene flow facilitated by human activities causing significant economic losses farmers. To better understand manage infestations, we assembled annotated haploid genome P. studied troublesome field populations from Oregon, the largest producing region United States. The assembly resulted 1.35 Gb DNA sequence distributed among seven chromosome-scale scaffolds, revealing high content transposable elements, conserved synteny with annua , close relationship other C 3 grasses. A reduced-representation sequencing analysis revealed limited genetic diversity suggested potential human-assisted dispersal region. resources insights into provided this study will improve management strategies enable development molecular detection tests for contaminated lots limit seed-mediated flow. These should also be beneficial breeders seeking desirable traits varieties help guide breeding efforts crops enhance resiliency ecosystems under climate change. Significance statement population genomic analyses provide crucial weedy contribute valuable resource plant science community.

Language: Английский

Current status of community resources and priorities for weed genomics research DOI Creative Commons
Jacob E. Montgomery, Sarah Morran, Dana R. MacGregor

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 27, 2024

Abstract Weeds are attractive models for basic and applied research due to their impacts on agricultural systems capacity swiftly adapt in response anthropogenic selection pressures. Currently, a lack of genomic information precludes elucidate the genetic basis rapid adaptation important traits like herbicide resistance stress tolerance effect evolutionary mechanisms wild populations. The International Weed Genomics Consortium is collaborative group scientists focused developing resources impact into sustainable, effective weed control methods provide insights about assist crop breeding.

Language: Английский

Citations

15
The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance DOI Creative Commons
Caio A. C. G. Brunharo, Aidan W. Short, Lucas K. Bobadilla

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 26, 2025

ABSTRACT Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution herbicide provides an excellent opportunity to study genetic and physiological basis phenotype evolutionary responses human‐mediated selection pressures. Lolium multiflorum is a ubiquitous weed that evolved repeatedly around world various cropping systems. We assembled annotated chromosome‐scale genome L. elucidated architecture paraquat by performing quantitative trait locus analysis, genome‐wide association studies, divergence analysis transcriptome analyses from paraquat‐resistant ‐susceptible plants. identified two regions on chromosome 5 were associated with resistance. These both showed evidence positive among resistant populations we sampled, but effects this differed, implying complex history. In addition, these contained candidate genes encoded cellular transport functions, including novel multidrug toxin extrusion (MATE) protein cation transporter previously shown interact polyamines. Given cultivated species, genomic resources generated will prove valuable wide spectrum plant science community. Our work contributes growing body knowledge underlying ecological dynamics rapid adaptation strong anthropogenic pressure could help initiate efforts improve management practices long term more agriculture.

Language: Английский

Citations

1
The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed DOI Creative Commons
Martin Laforest, Sara L. Martin, Katherine Bisaillon

et al.

The Plant Genome, Journal Year: 2024, Volume and Issue: 17(2)

Published: March 13, 2024

Abstract Ambrosia artemisiifolia and trifida (Asteraceae) are important pest species the two greatest sources of aeroallergens globally. Here, we took advantage a hybrid to simplify genome assembly present chromosome‐level assemblies for both species. These show high levels completeness with Benchmarking Universal Single‐Copy Ortholog (BUSCO) scores 94.5% A. 96.1% long terminal repeat (LTR) Assembly Index values 26.6 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in 50,203 . More than half is composed repetitive elements, 62% 69% Single copies herbicide resistance‐associated PPX2L , HPPD ALS found, while EPSPS gene identified; this latter observation may reveal possible mechanism resistance glyphosate. Ten 12 main allergenicity also localized, some forming clusters several copies, especially evolution structure has differed among these undergone greater rearrangement, possibly result chromoplexy. In contrast, retains that makes allotetraploidization most recent common ancestor Heliantheae Alliance clearest feature its genome. When compared other species, allowed us reconstruct ancestor's karyotype—a key step furthering our understanding diversification economically allergenically group.

Language: Английский

Citations

7
New insight into Poa annua control with clethodim from the dose-response study using several grass species and ACCase gene expression study DOI

Kensuke Ohta,

Yoshinobu Jin,

Yoshinao Sada

et al.

Pesticide Biochemistry and Physiology, Journal Year: 2025, Volume and Issue: 208, P. 106288 - 106288

Published: Jan. 6, 2025

Language: Английский

Citations

0
Chromosome‐scale genome assembly of Poa trivialis and population genomics reveal widespread gene flow in a cool‐season grass seed production system DOI Creative Commons
Caio A. C. G. Brunharo, Christopher W. Benson, David R. Huff

et al.

Plant Direct, Journal Year: 2024, Volume and Issue: 8(3)

Published: March 1, 2024

Abstract Poa trivialis (L.) is a cool‐season grass species found in various environments worldwide. In addition to being desired turfgrass species, it common weed of agricultural systems and natural areas. As weed, an important contaminant commercial seed lots, resulting widespread gene flow facilitated by human activities causing significant economic losses farmers. To better understand manage infestations, we assembled annotated haploid genome P. studied troublesome field populations from Oregon, the largest producing region United States. The assembly resulted 1.35 Gb DNA sequence distributed among seven chromosome‐scale scaffolds, revealing high content transposable elements, conserved synteny with annua , close relationship other C 3 grasses. A reduced‐representation sequencing analysis revealed limited genetic diversity suggested potential human‐assisted dispersal region. resources insights into provided this study will improve management strategies enable development molecular detection tests for contaminated lots limit seed‐mediated flow. These should also be beneficial breeders seeking desirable traits varieties help guide breeding efforts crops enhance resiliency ecosystems under climate change. Significance Statement: population genomic analyses provide crucial weedy contribute valuable resource plant science community.

Language: Английский

Citations

3
The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants DOI Creative Commons

Carlos de Tomás,

Carlos M. Vicient

Epigenomes, Journal Year: 2023, Volume and Issue: 8(1), P. 2 - 2

Published: Dec. 27, 2023

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in genome or create new copies themselves other positions genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, duplications. Host organisms have evolved a set mechanisms suppress TE activity counter threat that they pose integrity. includes epigenetic silencing TEs mediated by process RNA-directed DNA methylation (RdDM). In most cases, machinery is very efficient for vast majority TEs. However, there specific circumstances which evade such mechanisms, example, variety biotic abiotic stresses vitro culture. Hybridization also proposed as an inductor proliferation. fact, discoverer transposons, Barbara McClintock, first hypothesized interspecific hybridization provides "genomic shock" inhibits control leading mobilization studies carried out on this topic yielded diverse results, showing some cases total absence being limited only families. Here, we review current knowledge about impact plants possible implications changes mechanisms.

Language: Английский

Citations

8
The International Weed Genomics Consortium: Community Resources for Weed Genomics Research DOI Creative Commons

Jacob S. Montgomery,

Sarah Morran, Dana R. MacGregor

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 20, 2023

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

Language: Английский

Citations

7
The genome ofLolium multiflorumreveals the genetic architecture of paraquat resistance DOI Creative Commons
Caio A. C. G. Brunharo, Aidan W. Short, Lucas K. Bobadilla

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 2, 2024

SUMMARY - Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution herbicide provides an excellent opportunity to study genetic and physiological basis phenotype evolutionary responses human-mediated selection pressures. Lolium multiflorum is a ubiquitous weed that evolved repeatedly around world various cropping systems. We assembled annotated chromosome-scale genome L. elucidated architecture paraquat by performing quantitative trait loci analysis, genome-wide association studies, divergence transcriptome analyses from paraquat-resistant -susceptible populations. Results suggested two regions chromosome 5 were associated with resistance. contain candidate genes encode cellular transport functions, including novel multidrug toxin extrusion (MATE) protein, cation transporter previously shown interact polyamines. Our results reveal identified promising future functional studies. Given cultivated species, genomic resources generated will prove valuable wide spectrum plant science community.

Language: Английский

Citations

1
Differences in the genetic diversity and genome size between two ecotypes of Imperata cylindrica in Japan DOI Creative Commons
Yasuyuki Nomura, Yoshiko Shimono, Atsushi J. Nagano

et al.

Plant Species Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 29, 2024

Abstract Understanding genomic characteristics, such as genetic diversity and genome size, is important because they relate to species ecotype performance. Imperata cylindrica has two ecotypes, the common type (C‐type) early‐flowering (E‐type), which differ in their ecological characteristics distribution ranges Japan. This study aimed elucidate of C‐type E‐type ecotypes I. throughout Japan, using multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq) method. Genome‐wide single‐nucleotide polymorphism data analysis revealed that had greater clearer isolation distance than E‐type. Additionally, exhibited clear differentiation between southern part Amami Oshima other populations, consistent with differences its life history. The also a smaller E‐type, may contribute faster plant growth seed mass, compared larger These phenomena were C‐type. results showed genetically, highlighting necessity for different guidelines each conservation use revegetation.

Language: Английский

Citations

0
Correction: Homoeologous evolution of the allotetraploid genome of Poa annua L DOI Creative Commons
Christopher W. Benson,

Matthew R Sheltra,

Peter J. Maughan

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: July 18, 2023

Language: Английский

Citations

0