Analysis of the complete plastomes of Bidens pilosa L. 1753 (Asteraceae, Coreopsideae) from Beijing, China reveals high genetic diversity and possible misidentifications

Figures & data

Figure 1. Panorama (A) and detail (B) photos of Bidens pilosa. The photos were shot by Liqiang Wang and the coordinates of the plant was E116.278965, N40.041831. Main identifying traits: Capitulum, margin with tongue-like flower 5–7; tongue elliptic obovate, white, 5–8 mm long; apex obtuse or notched.

Figure 2. Schematic map of overall features of the Bidens pilosa plastome. The map contains six tracks in default. From the center outward, the first track shows the dispersed repeats. The dispersed repeats consist of direct (D) and Palindromic (P) repeats, connected with red and green arcs. The second track shows the long tandem repeats as short blue bars. The third track shows the short tandem repeats or microsatellite sequences as short bars with different colors. The colors, the type of repeat they represent, and the description of the repeat types are as follows. Black: c (complex repeat); Green: p1 (repeat unit size = 1); Yellow: p2 (repeat unit size = 2); Purple: p3 (repeat unit size = 3); Blue: p4 (repeat unit size = 4); Orange: p5 (repeat unit size = 5); Red: p6 (repeat unit size = 6). The small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions are shown on the fourth track. The GC content along the genome is plotted on the fifth track. The genes are shown on the sixth track. The optional codon usage bias is displayed in the parenthesis after the gene name. Genes are color-coded by their functional classification. The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively. The functional classification of the genes is shown in the bottom left corner.

Figure 3. The Maximum-Likelihood phylogeny of Bidens pilosa and its close relatives using 70 common CDS sequences. The bootstrap values based on 1000 replicates were shown on each node in the cladogram tree. The corresponding phylogram tree was shown in the upper right corner (Dots represented Bidens species). The 45 Bidens species Heliantheae alliance were downloaded from GenBank, which were B. pilosa (MZ127828), B. pilosa (MN433104) (Knope et al. 2020), B. alba var. radiata (MW551952) (Wu et al. 2022), B. pilosa (MW551953) (Wu et al. 2022), B. alba var. radiata (MW551955) (Wu et al. 2022), B. alba var. radiata (MZ127826), B. bipinnata (MZ127827), B. alba var. radiata (MN433106), B. bipinnata (MW551954), B. bipinnata (MW551957), B. bipinnata (MW551949), B. bipinnata (MW551956), B. biternata (MW691202), B. biternata (MW551958) (Wu et al. 2022), B. parviflora (MW551948) (Wu et al. 2022), B. hillebrandiana subsp. polycephala (MN433116) (Knope et al. 2020), B. forbesii subsp. kahiliensis (MN433094) (Knope et al. 2020), B. cosmoides (MN433115) (Knope et al. 2020), B. forbesii subsp. forbesii (MN433028) (Knope et al. 2020), B. conjuncta (MN433099) (Knope et al. 2020), B. campylotheca subsp. pentamera (MN433107) (Knope et al. 2020), B. menziesii subsp. menziesii (MN433101) (Knope et al. 2020), B. campylotheca subsp. campylotheca (MN433029) (Knope et al. 2020), B. amplectens (MN433103) (Knope et al. 2020), B. molokaiensis (MN433097) (Knope et al. 2020), B. wiebkei (MN433098) (Knope et al. 2020), B. valida (MN433092) (Knope et al. 2020), B. cervicata (MN433100) (Knope et al. 2020), B. hawaiensis (MN433095) (Knope et al. 2020), B. micrantha subsp. ctenophylla (MN433114) (Knope et al. 2020), B. menziesii subsp. filiformis x B. micrantha subsp. ctenophylla (MN433096) (Knope et al. 2020), B. menziesii subsp. filiformis (MN433110) (Knope et al. 2020), B. micrantha subsp. kalealaha (MN433102) (Knope et al. 2020), B. sandvicensis subsp. confusa (MN433091) (Knope et al. 2020), B. sandvicensis subsp. sandvicensis (MN433093) (Knope et al. 2020), B. asymmetrica (MN433105) (Knope et al. 2020), B. macrocarpa (MN433111) (Knope et al. 2020), B. sandvicensis (MN433113) (Knope et al. 2020), B. torta (MN433112) (Knope et al. 2020), B. mauiensis (MN433090) (Knope et al. 2020), B. schimperi (MN433108) (Knope et al. 2020), B. pachyloma (MN433109) (Knope et al. 2020), B. pilosa (MN729611) (Lin et al. 2018), B. tripartita (MW331585) (Wu et al. 2022), B. pilosa (MN385242, generated in this study, labeled by bold font and a diamond), B. frondosa (MT178455) (Feifei Li et al. 2020). Another two species Lactuca sativa (KT272174) (Jiang et al. 2021) and Taraxacum mongolicum (MN164624) (Kim et al. 2016) from the Lactuceae served as the outgroups. Previous B. pilosa plastomes deposited in the GenBank were labeled by triangles. All B. pilosa species were located in three clades.

Table 1. Conservative sequences used for designing primers for amplifying potential molecular markers between two B. pilosa plastomes.

No.	Genbank accession no.	Forward primer region start-end	Inverse primer region start-end	Sequences for designing forward primers	Sequences for designing inverse primers	Potential molecular markers	K2P distance between two markers
1	MN385242	334–361	408–624	AAACTATGTAAGGCAAATAG TACTAAATAAAAAAAAGGAGCAATA	TATTGCTCCTTTTTTAGTTCAAAAACTCCTA TACAATCAGACCAAAGTCTTATCC ATTTGTAGATGGAGCTTCAATAGCAGCTAAGT CTAGAGGGAAATTATGAGCATTACGTTCATGC ATAACTTCCATACCAAGGTTAGCACGGTTAAT GATATCAGCCCAAGTGTTAATTACACGGCCTT GACTATCAACTACCGATTGGTTGAAATTGAAACC	AAAAAAAAGGAGCAATAGCTTCCCTCT TGATAAAACAAGAGGGCAT	21.02
	MN433104	349–376	423–639			AAAAAAAAGGAGCAATAACG CCCTCTTGTTTTATCAAGAGGGAAGC
2	MN385242	51,787–51,822	51,892–52,058	CGCTTGATTGTATTTAATCGACAG AATCAAGTCAAA	TTGATAGCCTCTACTCGTGTCCTAGCCCGTCG TAGAGCTAGATTTGCCTCAATTGTTTGTCTCT TTCCTTCAGCTTTTCTCAAAGCATCTTCCGCTA TTTCAAGAGTTTGCTGAGCTTCTTGTGGATCG ATGTCACTACTTTTCTCTGCATCATTTACTAAAACAGT	AAAAACAACCAAACATAGGGT GTATAAATTGAT GATGATTCGGACACACCGACT GGTTATGAAATGGCA	16.54
	MN433104	51,953–51,988	52,071–52,237			CAAAACAACCAAATATAATAATA TAATATAGGGTGTA TAAATTGATGATTATTCGGACAC ACCAACTAGTTATGAAATGGCG
3	MN385242	64,445–64,495	64,599–64,698	TGATAAGTGAGTTTCTAATAATTCATG AAATGAATTAGAATATTACCGCAA	GAAATTTTCTTCGATAAACGAAAAAGAACAACG AATGAAATAATTGGAATCACTAATGCATGCATT GTTGTATTAGATCGAAATCTGAAATCTGAAGGTT	TTGTAAGTAGATTTGAGATCTATAAATCTTTG TTATTCATAGTCGCTTTTTGTT GGAATCTTTTT TTATCTTTTAAGGAACGTCCAGTA ACAAGGAATAATAG	24.76
	MN433104	64,782–64,832	64,957–65,056			ATTTAAGTAGATTTGAGCTTTGT TATTCATAG TTGTATAAGCGCTTTTTGTTG AAATCTTTTTTT ATCTTTTCTTTTAAGGAATTG GTTTATCTTTTA AGGAATTGGTTAGTCGTCCA GTAACA
4	MN385242	66,686–66,736	66,779–66,835	AAGGGAGGAAAGAGAAAGAATAAAAGTGCATT CAACAGCTGTGAGACTCGG	AATTTCTATGGAAGTCGAATACAAACAGTGGT TCTAGGGAAAGAGTATTATACAAGA	ATTCAGGTTGGAATTAAATTAAT ATGAAATTTC TATTTATTA	26.35
	MN433104	67,024–67,074	67,119–67,175			GTTCAGTTTGGAATTGAATTAATATT CAATTTCTATGGAAATTC
5	MN385242	117,415–117,468	117,512–117,589	TATATTCATAATTATATTGATTAGGCGGCGAG AATTGTGTTTTAATTTATATTA	GATGATTTGAAAATATATAGATTCAAATTACTC CTTCGAGAGATTAGGCCAATAACTACATCTAC ATCAATCCATATC	ATATGAAAAATAGATTTCAGTCTATA TTTATTATTTGAAAATT	26.06
	MN433104	117,796–117,855	117,913–117,990			TATGAAAAATTTATTTCTTTTCTATAGT CTATATTGATGATTGATGATTTGAAAATG

MN385242: Beijing B. pilosa. MN433104: Hawaii B. pilosa.

Knope ML, Renee BM, Datlof EM, Gallaher TJ, Johnson MA. 2020. Insights into the evolutionary history of the Hawaiian bidens (Asteraceae) adaptive radiation revealed through phylogenomics. J Hered. 111(1):1–19.

 PubMed Web of Science ®Google Scholar

Wu L, Nie L, Guo S, Wang Q, Wu Z, Lin Y, Wang Y, Li B, Gao T, Yao H. 2022. Identification of medicinal Bidens plants for quality control based on organelle genomes. Front Pharmacol. 13:842131.

 PubMed Web of Science ®Google Scholar

Lin Y-X, Duan R-Y ,Tan Z-X, Ma Y-H, Wu H. 2018. The complete chloroplast genome of the invasive and Cd-hyperaccumulator herb Bidens pilosa L. (Asteraceae). Mitochondrial DNA Part B. 3(2):746–747.

 PubMed Web of Science ®Google Scholar

Feifei Li JZ, Xiaoyan L, Kexiao G, Caiyun Z. 2020. The complete chloroplast genome of an invasive herb Bidens frondosa L. (Asteraceae). Mitochondrial DNA B Res. 5(2):1769–1770.

 Web of Science ®Google Scholar

Jiang M, Li Y, Chen H, Wang B, Liu C. 2021. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa. Mitochondrial DNA B Res. 6(4):1498–1506.

 PubMed Web of Science ®Google Scholar

Kim JK, Park JY, Lee YS, Woo SM, Park HS, Lee SC, Kang JH, Lee TJ, Sung SH, Yang TJ. 2016. The complete chloroplast genomes of two Taraxacum species, T. platycarpum Dahlst. and T. mongolicum Hand.-Mazz. (Asteraceae). Mitochondrial DNA B Res. 1(1):412–413.

 PubMed Web of Science ®Google Scholar

Data availability statement

The plastome sequence has been deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/) with the accession number of MN385242 (https://www.ncbi.nlm.nih.gov/nuccore/MN385242). The associated BioProject, Bio-Sample and SRA numbers are PRJNA543381, SAMN16089020 and SRR12620715 (https://www.ncbi.nlm.nih.gov/sra/?term=SRR12620715).