Amaranthus palmeri is one of the most aggressive invasive weeds worldwide, causing severe yield losses in major crops and exhibiting widespread herbicide resistance. Although its nuclear genome has been extensively studied, the mitochondrial genome, which plays essential roles in stress responses and reproductive development, remains unexplored. In this study, we report the first complete assembly and annotation of the A. palmeri mitogenome. The circular mitochondrial genome is 348,126 bp long (GC content 42.8%) and contains 54 genes: 30 protein-coding, 21 tRNA, and 3 rRNA. Comparative analysis with A. tricolor revealed differences in codon usage, repeat elements, RNA editing (296 versus 311 C-to-U sites), and intracellular gene transfer. A total of 1,243 repeat elements were identified in A. palmeri, compared to 1,176 in A. tricolor. We analyzed genome structure and synteny among seven species in the family Amaranthaceae, and reconstructed phylogenetic trees for these seven and 16 additional representative taxa (23 total). This study presents the first assembly and annotation of the mitochondrial genome of A. palmeri, revealing codon bias, repeat elements, RNA editing, and intracellular gene transfer. These results provide valuable insights into mitochondrial genome evolution and inform the development of mitochondrial markers for species identification, population monitoring, and lineage tracking, thereby supporting the management of A. palmeri.
Zheng et al. (Fri,) studied this question.