A chromosome-level genome assembly of Amaranthus spinosus provides insights into its evolution and invasion

Several Amaranthus species native to the Americas have become widespread invasive weeds, posing threats to agricultural production and ecosystems worldwide. Amaranthus spinosus is a tropical America weed that has established populations across tropical, subtropical, and warm-temperate regions. However, limited genomic resources have constrained our understanding of its invasion history and adaptive evolution.

We generated a chromosome-level genome assembly of Amaranthus spinosus comprising 17 chromosomes, with a genome size of 420.11 Mb and 98.0% BUSCO completeness. Comparative genomics analyses identified Amaranthus palmeri as the closest relative and revealed expansion of cytochrome P450 (P450), UDP-glycosyltransferase (UGT), and glutathione S-transferase (GST) gene families, which may contribute to environmental adaptation. A genus-level pan-genome of eight Amaranthus species identified 24 274 orthologous gene families, including 13 410 common, 9366 dispensable, and 1498 species-specific orthogroups. Genome-wide single nucleotide polymorphisms (SNPs) analysis of 61 accessions from five geographic regions identified six genetic subpopulations, including two strongly differentiated subpopulations within the United States (USA-1 and USA-2). Demographic history inferred from genome-wide SNPs supported an invasion history originating in the Americas, followed by spread to China and Zimbabwe and subsequently dispersal to Kenya. Selective sweep analyses identified candidate genes involved in environmental adaptation, with the two Africa populations showing enrichment of adenosine triphosphate (ATP) binding cassette (ABC) transporters and stress-response genes.

The chromosome-level genome and genome-wide SNPs generated in this study provides insights into the invasion history and adaptive evolution of Amaranthus spinosus. These resources establish a valuable foundation for functional investigation of invasive traits and may facilitate the development of genomics-informed strategies for monitoring and managing invasive Amaranthus weeds. © 2026 Society of Chemical Industry.