A chromosome-scale genome assembly and annotation of the tetraploid herb 'epazote' (Dysphania ambrosioides).

Abstract

Epazote (Dysphania ambrosiodes L.) is a perennial plant from the tropics of the Americas and is of regional importance due to both culinary and medicinal applications. However, few genomic resources exist to facilitate the identification of genes and pathways underlying the production of functionally important compounds in epazote. Here, we present a chromosome-scale assembly of the tetraploid epazote genome using PacBio HiFi reads and Hi-C. The final genome assembly contains 191 scaffolds spanning a total length of 469.23 Mbp, with 98.17% of the total length in the 16 largest chromosome-scale scaffolds. A BUSCO analysis identified 99.01% of the universal, single-copy orthologs, indicating that the genome is largely complete. We identified 51.81% of the genome as repetitive and annotated 24,424 genes. Collinearity of homologous genes has degraded to the point that, with few exceptions, homoeologous chromosome pairs cannot be identified, suggesting that the whole-genome duplication in epazote is relatively old. Analysis of epazote and related species suggests that the whole-genome duplication in epazote is independent and is older than the whole-genome duplication in quinoa but younger than that of amaranth.