Complete chloroplast genome of the endemic Acanthophyllum aculeatum Schischk. from Uzbekistan: comparative and phylogenetic analyses

Chloroplast genomes provide important insights into plant phylogeny, genome evolution, and the development of molecular markers. In this study, we sequenced, assembled, and characterized the complete chloroplast genome of the endemic species Acanthophyllum aculeatum Schischk. from Uzbekistan. The complete chloroplast genome was 150,911 bp in length and exhibited a typical quadripartite structure consisting of one large single-copy (LSC) region, one small single-copy (SSC) region, and two inverted repeat (IR) regions. Genome annotation identified 126 genes, including 81 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes. Comparative nucleotide diversity analysis with Acanthophyllum coloratum Schischk. and Acanthophyllum pungens (Bunge) Boiss. revealed several highly variable regions, with petD , psbA , atpF , and psaA–ycf3 showing the highest levels of sequence variation. IR boundary analysis revealed an overall conserved plastome organization, with minor differences in junction positions among the three Acanthophyllum species. Phylogenetic analysis based on complete chloroplast genomes strongly supported a monophyletic clade comprising A. aculeatum , A. pungens , and A. coloratum , with 100% bootstrap support. These results provide a new chloroplast genomic resource for A. aculeatum and contribute to a better understanding of plastome variation and phylogenetic relationships within Acanthophyllum and Caryophyllaceae.

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