Characteristics of the completed chloroplast genome sequence of Xanthium spinosum : comparative analyses, identification
- PDF / 2,576,168 Bytes
- 14 Pages / 595.276 x 790.866 pts Page_size
- 79 Downloads / 185 Views
RESEARCH ARTICLE
Open Access
Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications Gurusamy Raman1, Kyu Tae Park1, JooHwan Kim2 and SeonJoo Park1*
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. Keywords: Nucleotide diversity, Divergence, Ambrosiinae: genetic markers, phylogenomics
Background The structure of the majority of the flowering plant chloroplast (cp) genome consists of a pair of inverted repeats (IRs), along with large single-copy (LSC) and small single-copy (SSC) regions, and cp genome size ranges from 107 to 280 kb [1, 2]. With the emergence of nextgeneration sequencing technology [3], complete cp genome sequences are being extensively used to improve phylogenetic resolution at the interspecific level [4]. In * Correspondence: [email protected] 1 Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea 38541 Full list of author information is available at the end of the article
addition, cp genomes have been found to contain polymorphic regions generated through genomic expansion, contraction, inversion, or gene rearrangement, and such sequences have been widely used as an effective tool for plant phylogenomic analyses [5]. 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]. It is native to South America and has been introduced to Canada, the United States, Central and South America, parts of Africa, the Middle East, Russia, China, Australia, and the Korean Peninsula [7–10]. The genus Xanthium has been widely used for
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit t
Data Loading...
