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. 2023 Mar 14;24(1):113.
doi: 10.1186/s12864-023-09195-7.

Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa

Danchun Zhang  1   2 , Jiajun Tu  1   2 , Xiaoxia Ding  1   2 , Wan Guan  3 , Lu Gong  1   2   3 , Xiaohui Qiu  1   2   4 , Zhihai Huang  5   6 , He Su  7   8   9
Affiliations

Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa

Danchun Zhang et al. BMC Genomics. .

Abstract

Chloroplast genomes for 3 Bidens plants endemic to China (Bidens bipinnata Linn., Bidens pilosa Linn., and Bidens alba var. radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found in Bidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss of clpP and psbD, IR expansion and contraction were detected in these Bidens plants. It seems that ndhE, ndhF, ndhG, and rpl32 from the Bidens plants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3 Bidens plants clustered together and further formed molophyletic clade with other Bidens species, indicating Bidens plants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions of ndhD-ccsA, ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA, petN-psbM were candidate markers of molecular identification for Bidens plants. This study may provide useful information for genetic diversity analysis and molecular identification for Bidens species.

Keywords: Bidens alba; Bidens bipinnata; Bidens pilosa; Chloroplast genome; Phylogeny.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Chloroplast genome map of Bidens pilosa
Fig. 2
Fig. 2
Comparison of the boundaries of the LSC, SSC and IR regions. JLB: junction between LSC and IRb; JSB: junction between SSC and IRb; JSA: junction between. SSC and IRa; JLA: junction between LSC and IRa
Fig. 3
Fig. 3
Comparison of five chloroplast genomes using mVISTA by taking B. pilosa sequence as a reference. The lower left corner is the color coding of gene function, grey arrows indicate the orientation of genes, red bars represent conserved non-coding sequences, purple bars represent exons, and blue bars represent introns. The y-axis represents the percentage identity (shown: 50–100%)
Fig. 4
Fig. 4
Analysis of simple sequence repeats (SSRs) in the Bidens chloroplast genomes. A. different SSR types detected in three genomes. B. frequency of identified SSR motifs in different repeat class types
Fig. 5
Fig. 5
Analysis of repeated sequences in Bidens chloroplast genomes. C, F, P and R indicate the repeat types: complement repeat, forward repeat, reverse repeat and palindromic repeat
Fig. 6
Fig. 6
Pairwise Ka/Ks ratios in different genes. The scale factors associated with each value are displayed on the right side of the graph. The color close to red indicates that the gene has a high Ka/Ks ratio. Red indicates positive selection that is significantly enriched, while blue indicates negative selection that is significantly reduced. See Table S7 for abbreviations
Fig. 7
Fig. 7
The phylogenetic tree reconstruction base ML
See this image and copyright information in PMC

References

    1. Knope ML, Funk VA, Johnson MA, et al. Dispersal and adaptive radiation of Bidens (Compositae) across the remote archipelagoes of Polynesia. J Syst Evol. 2020;58(6):805–822. doi: 10.1111/jse.12704. - DOI
    1. Sun Y, Zhou Q, Wang L, et al. Cadmium tolerance and accumulation characteristics of Bidens pilosa L. as a potential Cd-hyperaccumulator. J Hazard Mater. 2009;161(2–3):808–814. doi: 10.1016/j.jhazmat.2008.04.030. - DOI - PubMed
    1. Li X, Tian L, Li B, et al. Polyaspartic acid enhances the Cd phytoextraction efficiency of Bidens pilosa by remolding the rhizospheric environment and reprogramming plant metabolism. Chemosphere. 2022;307(Pt 3):136068. doi: 10.1016/j.chemosphere.2022.136068. - DOI - PubMed
    1. Xuan TD, Khanh TD. Chemistry and pharmacology of Bidens pilosa: an overview. J Pharm Investig. 2016;46(2):91–132. doi: 10.1007/s40005-016-0231-6. - DOI - PMC - PubMed
    1. Bartolome AP, Villasenor IM, Yang WC. Bidens pilosa L. (Asteraceae): Botanical Properties, Traditional Uses, Phytochemistry, and Pharmacology. Evid Based Complement Alternat Med. 2013;2013:340215. doi: 10.1155/2013/340215. - DOI - PMC - PubMed

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