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Background  The invasive species  Xanthium spinosum  has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.    Results  Here, the complete chloroplast (cp) genome sequence of  X. spinosum  was assembled and analyzed. The cp genome of  X. spinosum  was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that  X. spinosum  contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that  Parthenium  is a sister clade to both  Xanthium  and  Ambrosia  and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value.    Conclusion  The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus  Xanthium .

bmc genomics

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications