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

Kyu Tae Park,Joo-Hwan Kim,Gurusamy Raman,SeonJoo Park

doi:10.1186/s12864-020-07219-0

Kyu Tae Park, Joo-Hwan Kim + Show 2 more

Open Access

https://doi.org/10.1186/s12864-020-07219-0

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Journal: BMC Genomics	Publication Date: Dec 1, 2020
Citations: 21	License type: open-access

Affiliation: Yeungnam University, Gachon University

Abstract

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

Highlights

The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years
An intact copy of the rps19 gene was present in the large single-copy (LSC)/IRb borders of X. spinosum, A. artemisiifolia, and P. argentatum, as well as a shared 95 bp to 119 bp sequence in the IRb region adjacent to the rpl2 gene
The X. sibiricum rps19 gene was completely shifted to the LSC region, 71 bp away from the IRb region, despite the rpl2 gene being present at the LSC/IRb border

Summary

Introduction

The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. No extensive molecular studies of this plant have been conducted. In. The invasive species Xanthium spinosum belongs to the family Asteraceae and is within the subtribe Ambrosiinae (Heliantheae), which includes annual and perennial herbaceous plants [6]. Raman et al BMC Genomics (2020) 21:855 various traditional medicinal treatments in multiple countries [11]. Parts of the X. spinosum plant are used for the treatment of cancer and diarrhea [12, 13], intermittent fever related to hydrophobia and rabies [14], and rheumatoid arthritis [15], and have antibacterial [14] and antiviral properties [14, 16,17,18]. Several antimicrobial substances and their functions have been studied in X. spinosum over the past five decades, no exclusive genetic or genomic studies have been conducted to date

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