Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny

SIMPLE SUMMARY: The genus Lycoris (Amaryllidaceae) comprises about 20 species with high ornamental and medicinal value. However, germplasm identification is still difficult due to frequent interspecific hybridization and intraspecific morphological variation within this genus. Plastid genome sequencing has been proven to be a useful tool to identify closely related species and is widely used in the field of plant evolution and phylogeny. In the present study, we provided four chloroplast genomes of Lycoris and retrieved seven published species in the genus for comparative genomics and phylogenetic analyses. All these chloroplast genomes possess the typical quadripartite structure with conserved genome arrangement and gene content, yet their lengths varied due to expansion/contraction of the IR/SC boundaries. Phylogenetic relationships within Lycoris were resolved with high resolution using complete cp genome sequences. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus. ABSTRACT: The genus Lycoris (Amaryllidaceae) consists of about 20 species, which is endemic to East Asia. Although the Lycoris species is of great horticultural and medical importance, challenges in accurate species identification persist due to frequent natural hybridization and large-scale intraspecific variation. In this study, we sequenced chloroplast genomes of four Lycoris species and retrieved seven published chloroplast (cp) genome sequences in this genus for comparative genomic and phylogenetic analyses. The cp genomes of these four newly sequenced species were found to be 158,405–158,498 bp with the same GC content of 37.8%. The structure of the genomes exhibited the typical quadripartite structure with conserved gene order and content. A total of 113 genes (20 duplicated) were identified, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. Phylogenetic analysis showed that the 11 species were clustered into three main groups, and L. sprengeri locate at the base of Lycoriss. The L. radiata was suggested to be the female donor of the L. incarnata, L. shaanxiensis, and L. squamigera. The L. straminea and L. houdyshelii may be derived from L. anhuiensis, L. chinensis, or L. longituba. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus.