比较叶绿体基因组分析揭示金荞麦复合群的精细系统发育框架与隐存多样性

Abstract

Background/Objectives:TheFagopyrum dibotryscomplex 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 atycf4–cemAandndhF–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 theF. dibotryscomplex and identifies informative chloroplast markers, providing a genomic foundation for reliable species delimitation, evolutionary inference, and conservation management of this medicinal lineage.