Structural characterization of the plastid genome and comparative mitochondrial genomics of Eupatorium lindleyanum...

Eupatorium lindleyanum is a widely utilized traditional medicinal plant with diverse pharmacological activities, extensive distribution, and abundant resources, making it a promising candidate for industrial and scientific research. However, limited genomic resources and unclear genetic relationships have hindered its development. To date, molecular studies on E. lindleyanum are scarce, and no detailed mitochondrial genome analyses have been reported for congeneric species.

In this study, we present the first complete assembly and annotation of the mitochondrial and plastid genomes of E. lindleyanum, investigating their potential for phylogenetic reconstruction within Asteraceae. Using Illumina NovaSeq and Nanopore PromethION platforms, 13.4 Gb and 12 Gb of raw sequencing data were generated, respectively. The mitochondrial genome of E. lindleyanum is a 299,285 bp circular DNA molecule with a GC content of 45.06%, encoding 32 unique protein-coding genes, 17 tRNA genes, and 3 rRNA genes. The plastid genome of E. lindleyanum, a typical quadripartite circular structure, is 151,377 bp in length with a GC content of 37.60%, comprising 80 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Codon usage analysis revealed a preference for A or T at the third codon position in mitochondrial genes. The mitochondrial genome contains 73 simple sequence repeats, 31 tandem repeats, 274 dispersed repeats, and 504 predicted RNA editing sites. Additionally, 11,245 bp of homologous sequences were identified between the mitochondrial and plastid genomes, accounting for 3.76% of the mitochondrial genome. Comparative analysis with E. chinense demonstrated significant structural variation within mitochondrial genomes of the Eupatorium genus, highlighting potential evolutionary mechanisms such as gene loss and functional compensation. Phylogenetic reconstruction using mitochondrial genome data further confirmed its utility in resolving evolutionary patterns and relationships, providing complementary insights to traditional plastid-based approaches.

These findings provide foundational genomic resources for E. lindleyanum, offering critical insights into the evolution of mitochondrial genomes in the genus Eupatorium. This study also contributes to understanding the evolutionary mechanisms and environmental adaptability of E. lindleyanum, paving the way for future research on its genetic and functional diversity.