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

• Published in: BMC genomics Vol. 21; no. 1; p. 855
• Main Authors: Raman, Gurusamy, Park, Kyu Tae, Kim, Joo-Hwan, Park, SeonJoo
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 02-12-2020; BioMed Central; BMC
• Subjects: Ambrosiinae: genetic markers, phylogenomics; Botanical research; Chloroplasts; Comparative analysis; Compositae; Divergence; Divergent evolution; Flowers & plants; Genes; Genetic aspects; Genome, Chloroplast; Genomes; Genomics; Herbal medicine; Introduced species; Invasive species; Microsatellite Repeats; Mutation; Natural history; Nucleotide diversity; Nucleotide sequence; Phylogenetics; Phylogeny; Proteins; rRNA; Spacer region; Structure; Traditional Chinese medicine; Transfer RNA; tRNA; Xanthium; Xanthium - genetics; Xanthium spinosum; South Korea; South America; Ambrosiinae: genetic markers, phylogenomics; Nucleotide diversity; Divergence
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-07219-0

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.
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.
The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.