Abstract

Zephyranthes carinata is a widely distributed medicinal and ornamental plant. Here, we reported the first complete chloroplast genome using high-throughput sequencing technology. The genome was a molecule with a typical quadripartite structure and spanned 158,355 bp in size, comprising an LSC region of 86,576 bp, an SSC region of 18,313 bp, and two IRs of 26,733 bp each. Its overall GC content was 37.81%. It was annotated with 129 functional genes, including 86 protein-coding, 35 tRNA, and eight rRNA genes. Phylogenetic analysis identified Z. carinata as a basal lineage within the Hippeastrinae subtribe of Amaryllidaceae family, suggesting its ancestral status. This chloroplast genome provides a valuable genetic resource for species identification, population genetics, and phylogenetic studies in Amaryllidaceae.