Objective A detailed analysis of the chloroplast (CP) genome structure and sequence characteristics of Thalictrum plants was conducted to screen for candidate molecular markers, laying the foundation for addressing the controversies in species classification and identification of Thalictrum species caused by their wide distribution and complex phenotypic variations. Methods The CP genome sequencing and structural analysis of Thalictrum finetii and Thalictrum cultratum were performed for the first time using the Illumina HiSeq4000 sequencing platform. Subsequently, a comprehensive analysis was performed simple sequence repeats (SSRs), inverted repeat (IR) region boundary structures, nucleotide diversity (Pi) and other characteristics, combined with the chloroplast (CP) genome data of 14 congeneric species published in the NCBI. Finally, by integrating the CP genome data of 45 species from 10 genera within the Ranunculaceae family, an ML phylogenetic tree was constructed and phylogenetic analysis was performed. Results The chloroplast genome lengths of T. finetii and T. cultratum are 155 953 bp and 155 901 bp, respectively, both exhibiting a typical circular quadripartite structure. A total of 131 genes were identified, with codon usage bias showing a predominant preference for A/U endings. While the CP genomes of Thalictrum species demonstrate high conservation in both gene count and genomic structure, specific differences are observed in the lengths of particular genes at the IRs/LSC and IRs/SSC boundaries in certain species. In terms of sequence variation, the divergence in non-coding sequences was significantly higher than that in coding sequences, with the IR regions exhibiting markedly lower variability compared to the LSC and SSC regions. Ultimately, ten hypervariable regions (ndhF-rpl32, ycf1, petN-psbM, ndhC-trnV, trnT-trnL, trnS-psbZ, ndhG-ndhI, ndhD, infA, rpl16) were identified as candidate DNA barcodes for the Thalictrum genus. Through systematic evolutionary analysis, the evolutionary relationships among the species within the genus Thalictrum and the systematic evolutionary position of this genus in the Ranunculaceae family were clarified. Conclusion This study presents the first report of the chloroplast genomes of T. finetii and T. cultratum, with a detailed analysis of the genomic structure and sequence characteristics of the Thalictrum genus. Ten hypervariable regions were identified as candidate DNA barcodes for species identification within Thalictrum. And a more comprehensive and reliable phylogenetic tree of the family Ranunculaceae was established.

Thalictrum finetii B. Boivin  /  Thalictrum cultratum Wall.  /  chloroplast genome  /  Thalictrum L.  /  phylogenetic analysis