New insights into the phylogenetic relationships among wild onions (, Amaryllidaceae), with special emphasis on the subgenera and , as revealed by plastomes.

The genus , with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within have long been not resolved. Based on 76 species of (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera and . We retrieved the three major evolutionary lines within and found that the two subgenera and are monophyletic whereas others are highly polyphyletic (e.g., , , , and ). Within the subgenus , two strongly supported sublineages in East Asian and Eurasian-American were found. in North America belonged to the Eurasian clade. The distinct taxonomic status of and its sister taxon were further determined. In subg. , the Ulleung Island endemic shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic . Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian (subg. ) and sister relationship between and was suggested.