ArticleBMC biology2017
Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.
Article in BMC biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed, 146 citations in OpenAlex.
- Identification of a candidate self-incompatibility locus in beet (Beta vulgaris).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Unravelling genetic diversity in grain amaranth (Amaranthus hypochondriacus L.) core accessions using genome-wide SNP markers.Molecular genetics and genomics : MGG · 2026Article
- Genome-wide identification and characterization of the stress-associated proteins (SAPs) gene family in Amaranthus palmeri S. Watson.Molecular biology reports · 2026Article
- Article
- Genetic architecture of seed protein composition in grain amaranth (Frontiers in nutrition · 2026Article
- QTL mapping of key phenological and morphological traits in grain amaranth (Breeding science · 2025Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Genome-wide analysis of NAC transcription factors in grain amaranth reveals structural diversity and regulatory features.Scientific reports · 2025Article
- A chromosome-scale genome assembly and annotation of the tetraploid herb "epazote" (Dysphania ambrosioides).G3 (Bethesda, Md.) · 2025Article
- Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity.BMC genomics · 2025Article
- The pomegranate (Punica granatum L. cv. 'Wonderful') genome and P. protopunica shed light on pomegranate domestication. Is Daru a wild stock?BMC genomics · 2025Article
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
- Genetic distances and genome wide population structure analysis of a grain amaranth (Amaranthus hypochondriacus) diversity panel using genotyping by sequencing.Scientific reports · 2025Article
- Bioinformatics Analysis Reveals PPR Genes Modulation by Ahyp-miR0005 Under Abiotic Stress Across Diverse Plant Species.Plants (Basel, Switzerland) · 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
- The evolution of separate sexes in waterhemp is associated with surprising chromosomal diversity and complexity.PLoS biology · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational 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
- Exploring the hidden treasure in arid regions: pseudocereals as sustainable, climate-resilient crops for food security.Frontiers in plant science · 2025Review
12 more citing papers are in PubMed but not listed here.
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6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species.
resultsUtilizing single-molecule, real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C) to close assembly gaps and scaffold contigs, respectively, we improved our previously reported Illumina-based assembly to produce a chromosome-scale assembly with a scaffold N50 of 24.4 Mb. The 16 largest scaffolds contain 98% of the assembly and likely represent the haploid chromosomes (n = 16). To demonstrate the accuracy and utility of this approach, we produced physical and genetic maps and identified candidate genes for the betalain pigmentation pathway. The chromosome-scale assembly facilitated a genome-wide syntenic comparison of amaranth with other Amaranthaceae species, revealing chromosome loss and fusion events in amaranth that explain the reduction from the ancestral haploid chromosome number (n = 18) for a tetraploid member of the Amaranthaceae.
conclusionsThe assembly method reported here minimizes cost by relying primarily on short-read technology and is one of the first reported uses of in vivo Hi-C for assembly of a plant genome. Our analyses implicate chromosome loss and fusion as major evolutionary events in the 2n = 32 amaranths and clearly establish the homoeologous relationship among most of the subgenome chromosomes, which will facilitate future investigations of intragenomic changes that occurred post polyploidization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.