The complete chloroplast genomes of five species of Allium subg. Melanocrommyum (Amaryllidaceae)

Subgenus Melanocrommyum of the genus Allium (Amaryllidaceae) comprises morphologically diverse and taxonomically complex species, many of which are endemic to Central Asia. In this study, we sequenced and analyzed the complete chloroplast genomes of five species, A. alaicum, A. altissimum, A. giganteum, A. isakulii, and A. karataviense, representing five distinct taxonomic sections. All plastomes exhibited a typical quadripartite structure with conserved gene content. Genome sizes ranged from 151,960 to 152,725 bp. Codon usage showed bias toward AGA (Arg) and UUG (Leu), and a total of 79–90 SSRs and 423 long repeats were identified. Divergence hotspot regions included accD, ndhD, and rps4, while ycf2 was highly conserved but showed a high ω value, suggesting its possible adaptive evolution. Phylogenetic analysis based on protein-coding genes consistently resolved two major clades for the studied species, supporting the monophyly of the group and existing sectional classifications. This study provides valuable genomic data for Allium, highlights plastome evolution in Melanocrommyum, and identifies markers for future phylogenetic and evolutionary studies.