Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i>
<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 classi...
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| author | Jizhe Han Chuhang Lin Tingting Zhu Yonghui Liu Jing Yan Zhechen Qi Xiaoling Yan |
| author_facet | Jizhe Han Chuhang Lin Tingting Zhu Yonghui Liu Jing Yan Zhechen Qi Xiaoling Yan |
| author_sort | Jizhe Han |
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| description | <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. |
| format | Article |
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| spelling | doaj-art-ddb59cdb91134f5ca92a3677827ca35a2025-08-20T02:06:12ZengMDPI AGPlants2223-77472025-02-0114564910.3390/plants14050649Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i>Jizhe Han0Chuhang Lin1Tingting Zhu2Yonghui Liu3Jing Yan4Zhechen Qi5Xiaoling Yan6Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaZhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China<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.https://www.mdpi.com/2223-7747/14/5/649<i>Amaranthus</i> taxonomychloroplast genomegenome conservationspecies identificationphylogenetic analysescomparative genomics |
| spellingShingle | Jizhe Han Chuhang Lin Tingting Zhu Yonghui Liu Jing Yan Zhechen Qi Xiaoling Yan Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> Plants <i>Amaranthus</i> taxonomy chloroplast genome genome conservation species identification phylogenetic analyses comparative genomics |
| title | Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> |
| title_full | Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> |
| title_fullStr | Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> |
| title_full_unstemmed | Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> |
| title_short | Comprehensive Chloroplast Genomic Insights into <i>Amaranthus</i>: Resolving the Phylogenetic and Taxonomic Status of <i>A. powellii</i> and <i>A. bouchonii</i> |
| title_sort | comprehensive chloroplast genomic insights into i amaranthus i resolving the phylogenetic and taxonomic status of i a powellii i and i a bouchonii i |
| topic | <i>Amaranthus</i> taxonomy chloroplast genome genome conservation species identification phylogenetic analyses comparative genomics |
| url | https://www.mdpi.com/2223-7747/14/5/649 |
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