ArticleGenome biology and evolution2020
Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri.
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Non-triazine photosystem II inhibitors provide effective control of metabolic atrazine-resistant Amaranthus tuberculatus.Pest management science · 2026Article
- Extensive variation between chromosomes of North American and European hop.Nature communications · 2026Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
- Amaranth, the ancient pseudocereal: a promising crop for climate-resilient agriculture and healthy diets.Frontiers in plant science · 2026Review
- Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity.BMC genomics · 2025Article
- Genetic diversity and population structure of ALS-resistant Amaranthus hybridus across Brazil's primary soybean-growing regions.Pest management science · 2025Article
- Determination of the Mechanisms of MCPA Resistance inPlant direct · 2025Article
- Dynamic Genetic Changes Reveal: Intra-Lineage Diversity, Not Admixture, ExplainsInternational journal of molecular sciences · 2025Article
- Unraveling the Role of P450 Reductase in Herbicide Metabolic Resistance Mechanism.Plant direct · 2025Article
- Assessing and mining grain amaranth diversity for sustainable cropping systems.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Function of cytochrome P450 CYP72A1182 in metabolic herbicide resistance evolution in Amaranthus palmeri populations.Journal of experimental botany · 2025Article
- The evolution of separate sexes in waterhemp is associated with surprising chromosomal diversity and complexity.PLoS biology · 2025Article
- Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region.The Plant journal : for cell and molecular biology · 2025Article
- Current status of community resources and priorities for weed genomics research.Genome biology · 2024Review
- Weed biology and management in the multi-omics era: Progress and perspectives.Plant communications · 2024Review
- Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content.Plants (Basel, Switzerland) · 2024Article
- Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus.BMC plant biology · 2023Article
- Weed genomics: yielding insights into the genetics of weedy traits for crop improvement.aBIOTECH · 2023Review
- Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes.BMC biology · 2023Article
- Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning.Frontiers in plant science · 2023Article
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14 authors.
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Abstract
Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and coassembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, whereas genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.
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