Phylogenetic study and accurate identification of Tamarix species in China based on complete chloroplast genomes

BACKGROUND: Tamarix species play a significant ecological role in desert transformation and climate improvement, representing nearly 75% of Tamaricaceae. However, due to their high morphological variability and susceptibility to interspecific hybridization, Tamarix remains one of the most poorly classified genera among flowering plants, which has significantly impeded the utilization of Tamarix species in ecological restoration projects across desert regions. China is among the countries most severely affected by desertification. Therefore, this study aims to compare chloroplast genomes among Tamarix species distributed in China, clarify their phylogenetic relationships, and identify molecular markers for species identification. RESULTS: In this study, we obtained the complete chloroplast genomes (CPGs) of 16 Tamarix species (33 CPGs), 24 of which were newly generated. A total of 1,650 non-SSR-related indels and 1,428 non-indel-related SSRs were identified, with mononucleotide SSRs being the most abundant. Comparative analyses using mVISTA revealed high sequence similarity across Tamarix chloroplast genomes, indicating strong conservation, except for Tamarix androssowii (OR619632). Overall, inverted repeat (IR) and coding regions were more conserved than single-copy and noncoding regions. Several intergenic regions showed higher variability than commonly used universal DNA markers. Phylogenetic analyses strongly supported the monophyly of Tamarix with two Myricaria samples as outgroups. CONCLUSION: Using 35 CPGs, we reconstructed a well-resolved phylogeny of Tamarix. Variations in branch lengths and support values provide new insights into intrageneric relationships within the genus. The genomic resources generated in this study offer a valuable foundation for future research on population genetics, species identification, and conservation of Tamarix.