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Comparative Chloroplast Genome Analyses Reveal a Fine-Scale Phylogenetic Framework and Cryptic Diversity in the Fagopyrum dibotrys Complex (Polygonaceae)
| First Author: |
Wei, Yi-Ming |
| Abstract: |
Background/Objectives: The Fagopyrum dibotrys complex is a specialized high-altitude lineage in southwestern China with medicinal and breeding potential, but species delimitation remains unresolved. Methods: We sequenced 26 complete chloroplast genomes from the Hengduan Mountains to the Yunnan-Guizhou Plateau, analyzing genomic structures, variation patterns, and phylogenetic relationships. Results: All genomes exhibited typical quadripartite structures (152,213-160,302 bp), containing 133 genes (88 protein-coding, 8 rRNA, and 37 tRNA) with GC content of 37.9%. Collinearity analysis revealed highly conserved structures without structural rearrangements. Variations were concentrated in the large single-copy(LSC)/small single-copy(SSC) non-coding regions, with hotspots at ycf4-cemA and ndhF-rpl32. Codon usage showed an A/U bias, with leucine being most abundant and cysteine the least. Simple sequence repeats (SSRs) were predominantly mononucleotide repeats enriched in the LSC, while long repeats were mainly palindromic/forward. Maximum likelihood and Bayesian phylogenies consistently resolved three clades: Tibetan high-altitude specialists, limestone specialists, and a widespread Hengduan-Yunnan-Guizhou clade, with geographic clustering indicating isolation as the primary differentiation driver. Conclusions: This study refines the phylogenetic resolution of the F. dibotrys complex and identifies informative chloroplast markers, providing a genomic foundation for reliable species delimitation, evolutionary inference, and conservation management of this medicinal lineage. |
| Contact the author: |
Lei, SQ ;Li, B |
| Page Number: |
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| Issue: |
2 |
| Subject: |
Genetics & Heredity |
| Impact Factor: |
2.8 |
| Authors units: |
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| PubYear: |
2026 |
| Volume: |
17 |
| Publication Name: |
GENES |
| The full text link: |
10.3390/genes17020149 |
| ISSN: |
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| Download: |
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