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Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications
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Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications
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Journal Article
Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications
2020
Overview
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
.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
