Comprehensive Chloroplast Genomic Insights into Amaranthus: Resolving the Phylogenetic and Taxonomic Status of A. powellii and A. bouchonii

<i>Amaranthus</i>, a genus in Amaranthaceae, is divided into three subgenera-<i>Amaranthus</i>, <i>Acnida</i>, and <i>Albersia</i>-and contains approximately 70 to 80 species. Understanding its phylogenetic relationships is essential for species classification, genetic diversity assessment, and evolutionary studies. This knowledge is vital for improving <i>Amaranthus</i> utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 <i>Amaranthus</i> species across all three subgenera to characterize their genomic features and construct a comprehensive phylogenetic tree. Our aim was to elucidate the phylogenetic relationships within the genus and evaluate interspecific affinities among the subgenera. We also addressed the taxonomic ambiguity surrounding <i>A. bouchonii</i> and <i>A. powellii</i> to determine their distinct species within the genus. Chloroplast genome sizes ranged from 149,949 to 150,818 bp, with GC content varying between 36.52% and 36.63%. Comparative structural analyses confirmed highly conserved quadripartite structures, gene content, and organization, comprising 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat and codon usage analyses revealed conserved repeat patterns and a preference for codons ending in A or U. Selection pressure analysis indicated a predominantly purifying selection, with <i>matK</i> showing signs of positive selection, particularly in <i>A. spinosus</i>. Phylogenetic analysis of 80 protein-coding genes confirmed the monophyly of subgenus <i>Amaranthus</i> but found <i>Alberisa</i> and <i>Acnida</i> to be paraphyletic. Despite their morphological similarity, <i>A. bouchonii</i> and <i>A. powellii</i> were placed in separate clades within subgenus <i>Amaranthus</i>, with <i>A. bouchonii</i> clustering with <i>A. retroflexus</i>, and <i>A. powellii</i> aligning with the <i>A. hybridus</i> complex. Additionally, we identified 16 variable regions as potential molecular markers for species identification. Our study provides the most comprehensive <i>Amaranthus</i> chloroplast genome dataset to date, offering new insights into its evolutionary relationships and valuable genomic resources for taxonomy, germplasm management, and invasive risk assessment.