Abstract
Xanthium sibiricum has been used widely in Chinese medicine for many years. Although of medicinal value, some species in the Xanthium are reported to be toxic and thus correct identification is essential. Whereas previous identification methods based on molecular characteristics are insufficient for in-depth authentication, chloroplast genome sequences provide more information that can assist in genome-wide evolutionary research. In this study, we sequenced complete chloroplast (cp) genome of X. sibiricum using next-generation sequencing technology and the complete sequence was deposited in Genbank with the accession number MH473582. This is the first reported sequence for the complete cp genome of Xanthium. The complete X. sibiricum cp genome is 151,897 bp in length, comprising one pair of inverted repeats (IRs) of 24,905 bp, separated by one small single copy region (SSC; 17,900 bp) and one large single copy region (LSC; 84,187 bp). The genome contains 115 unique genes, which code for 81 proteins, four rRNAs and 30 tRNAs. All four rRNA genes and seven tRNA genes, ycf15, ycf2, rpl2, rps12, rpl23, ndhB and rps7, are duplicated in the IR regions. The X. sibiricum cp genome has 40 repeat sequences and 59 simple sequence repeat (SSR) loci. Both Maximum parsimony (MP) and maximum likelihood (ML) trees provide very strong bootstrap support (100%) for the sister relationship of X. sibiricum with Ambrosia in the subtribe Ambrosiinae. Our study provides molecular information for further studies with which to identify X. sibiricum among closely related species and other angiosperms.
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We thank two anonymous reviewers for their constructive comments and suggestions to improve our manuscript.
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This work was financially supported by the Excellent Doctor Innovation Project of Shaanxi Normal University (S2015YB03), the Fundamental Research Funds for the Central Universities (2016TS057), and the Fundamental Research Funds for the Central Universities (GK201604008; GK201702010; GK201701006); The key R & D plan of Shaanxi province (2018ZDXMSF-079), This work was supported in part by the National Natural Science Foundation of China (No. 61673251, No. 61760101).
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Online Resource 1. Commands used in cp genome assembly.
Online Resource 2. The list of taxa and accession numbers of the chloroplast genome sequences used in phylogenetic analysis.
Online Resource 3. Alignment of 46 concatenated protein-coding genes used in ML and MP analysis.
Online Resource 4. Complete plastome sequence of Xanthium sibiricum.
Online Resource 5. The simple sequence repeats in Xanthium sibiricum cp genome.
Online Resource 6. The maximum parsimony (MP) phylogenetic tree based on 46 protein-coding genes in the chloroplast genomes.
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Somaratne, Y., Guan, DL., Wang, WQ. et al. Complete chloroplast genome sequence of Xanthium sibiricum provides useful DNA barcodes for future species identification and phylogeny. Plant Syst Evol 305, 949–960 (2019). https://doi.org/10.1007/s00606-019-01614-1
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DOI: https://doi.org/10.1007/s00606-019-01614-1