Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications
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 ana...
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| Format: | Article |
| Language: | English |
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BMC
2020-12-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-07219-0 |
| _version_ | 1818928989113155584 |
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| author | Gurusamy Raman Kyu Tae Park JooHwan Kim SeonJoo Park |
| author_facet | Gurusamy Raman Kyu Tae Park JooHwan Kim SeonJoo Park |
| author_sort | Gurusamy Raman |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T03:37:40Z |
| format | Article |
| id | doaj.art-fd09cb08ab0342b98ad8bae88db8e94b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T03:37:40Z |
| publishDate | 2020-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-fd09cb08ab0342b98ad8bae88db8e94b2022-12-21T19:54:50ZengBMCBMC Genomics1471-21642020-12-0121111410.1186/s12864-020-07219-0Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implicationsGurusamy Raman0Kyu Tae Park1JooHwan Kim2SeonJoo Park3Department of Life Sciences, Yeungnam UniversityDepartment of Life Sciences, Yeungnam UniversityDepartment of Life Sciences, Gachon UniversityDepartment of Life Sciences, Yeungnam UniversityAbstract 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.https://doi.org/10.1186/s12864-020-07219-0Nucleotide diversityDivergenceAmbrosiinae: genetic markers, phylogenomics |
| spellingShingle | Gurusamy Raman Kyu Tae Park JooHwan Kim SeonJoo Park Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications BMC Genomics Nucleotide diversity Divergence Ambrosiinae: genetic markers, phylogenomics |
| title | Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications |
| title_full | Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications |
| title_fullStr | Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications |
| title_full_unstemmed | Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications |
| title_short | Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications |
| title_sort | characteristics of the completed chloroplast genome sequence of xanthium spinosum comparative analyses identification of mutational hotspots and phylogenetic implications |
| topic | Nucleotide diversity Divergence Ambrosiinae: genetic markers, phylogenomics |
| url | https://doi.org/10.1186/s12864-020-07219-0 |
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