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

Authors
Raman, G.Park, K.T.Kim, J.H.Park, S.J.
Issue Date
Dec-2020
Publisher
BMC
Keywords
Ambrosiinae: genetic markers, phylogenomics; Divergence; Nucleotide diversity
Citation
BMC GENOMICS, v.21, no.1
Journal Title
BMC GENOMICS
Volume
21
Number
1
URI
https://scholarworks.bwise.kr/gachon/handle/2020.sw.gachon/79407
DOI
10.1186/s12864-020-07219-0
ISSN
1471-2164
Abstract
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. © 2020, The Author(s).
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