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

作者：Jizhe Han, Chuhang Lin, Tingting Zhu, Yonghui Liu, Jing Yan, Zhe‐Chen Qi, Xiao‐Ling Yan · 发表于：Plants · 年份：2025 · DOI：10.3390/plants14050649 · 被引用次数：6 · 研究领域：Genomics and Phylogenetic Studies、Genetic diversity and population structure、Plant Pathogens and Fungal Diseases

Amaranthus, a genus in Amaranthaceae, is divided into three subgenera—Amaranthus, Acnida, and Albersia—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 Amaranthus utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 Amaranthus 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 A. bouchonii and A. powellii 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 matK showing signs of positive selection, particularly in A. spinosus. Phylogenetic analysis of 80 protein-coding genes confirmed the ...