Refining Arctium lappa chloroplast genomic resources through genome skimming and public data mining

Plastomes provide valuable resources for plant systematics, evolution, and molecular identification due to their conserved structure and uniparental inheritance. Arctium lappa (greater burdock) is an economically and medicinally important species, yet its chloroplast genomic diversity remains insufficiently characterized. In this study, we reconstructed the complete plastome of a naturalized A. lappa accession from Rochester, New York, USA, using a genome skimming approach, and expanded plastome sampling by mining publicly available Sequence Read Archive (SRA) datasets. High-quality Illumina reads were assembled using GetOrganelle and annotated with GeSeq, yielding circular plastomes with sizes ranging from 152,655 to 152,767 bp across bona fide A. lappa accessions. Comparative analyses revealed that a recently published plastome labeled as A. lappa is misidentified, instead corresponding to Pulsatilla chinensis , highlighting the need for careful validation of public genomic resources. Phylogenomic reconstruction based on concatenated chloroplast genes recovered all verified A. lappa accessions as a strongly supported monophyletic clade, with the Rochester accession forming a sister relationship to other sampled lineages. Notably, Arctium minus and Arctium tomentosum were nested within the broader A. lappa clade with extremely short branch lengths, suggesting close plastid relationships and potential taxonomic complexity within the genus. Together, this study refines chloroplast genomic resources for burdock, identifies informative plastid variation, and provides an expanded phylogenomic framework to support future studies in systematics, evolution, and species authentication.