Treffer: Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae).
Title:
Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae).
Authors:
Xue Y; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Qin S; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Xianyu Z; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Wang H; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Yu J; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Zhao X; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Liang X; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Li D; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China., Gai Y; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China. gaiyunpeng@bjfu.edu.cn.
Source:
Functional & integrative genomics [Funct Integr Genomics] 2025 Aug 27; Vol. 25 (1), pp. 175. Date of Electronic Publication: 2025 Aug 27.
Publication Type:
Journal Article; Comparative Study
Language:
English
Journal Info:
Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Berlin : Springer, c2000-
MeSH Terms:
References:
Almutairi MM (2021) Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern. Saudi J Biol Sci 28:4569–4574. (PMID: 343544428325026)
Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of Chloroplast genomes. Bioinformatics 34:3030–3031. (PMID: 29659705)
Barbosa ML, Alves M, Roque N (2023aa) Untangling the tribe Coreopsideae (Asteraceae) beyond taxonomic concepts. Acta Bot Brasilica 37.
Barbosa ML, Alves M, Roque N (2023b) Untangling the tribe Coreopsideae (Asteraceae) beyond taxonomic concepts. Acta Bot Brasilica 37:e20230068.
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583–2585. (PMID: 283984595870701)
Benitez-Villasenor A, Mendoza CG, Wanke S, Cevallos MP, Freire ME, Lemmon EM, Lemmon AR, Magallon S (2023) The use of anchored hybrid enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 181:107714. (PMID: 36708940)
Brinkman FS, Leipe DD (2001) Phylogenetic analysis. Bioinformatics: Practical Guide Anal Genes Proteins 2:349.
Camiolo S, Melito S, Porceddu A (2015) New insights into the interplay between codon bias determinants in plants. DNA Res 22:461–469. (PMID: 265462254675714)
Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, Chen S (2022) Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan plateau. BMC Plant Biol 22:195. (PMID: 354137909004202)
Cao Z, Yang L, Xin Y, Xu W, Li Q, Zhang H, Tu Y, Song Y, Xin P (2023) Comparative and phylogenetic analysis of complete Chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). Front Plant Sci 14:1205051. (PMID: 3748447610362447)
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. (PMID: 195059452712344)
Cauz-Santos LA (2025) Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms. New Phytologist.
Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC (2020) A repertory of rearrangements and the loss of an inverted repeat region in Passiflora Chloroplast genomes. Genome Biol Evol 12:1841–1857. (PMID: 327227487586853)
Chauhan BS, Ali HH, Florentine S (2019) Seed germination ecology of Bidens Pilosa and its implications for weed management. Sci Rep 9:16004. (PMID: 316908896831588)
Chetri BK, Senapati A, Sonu S, Shelke RG, Mitra S, Rangan L (2025) Comparative plastome analysis of apocynaceae with de Novo sequencing of Thevetia peruviana: insights into evolution and phylogeny. Trop Plant Biology 18:1–14.
Chiang YM, Chuang DY, Wang SY, Kuo YH, Tsai PW, Shyur LF (2004) Metabolite profiling and chemopreventive bioactivity of plant extracts from < i >Bidens Pilosa. J Ethnopharmacol 95:409–419. (PMID: 15507368)
Daniell H, Lin C-S, Yu M, Chang W-J (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17.
Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45.
Dobrogojski J, Adamiec M, Lucinski R (2020) The Chloroplast genome: a review. Acta Physiol Plant 42.
Doherty A, McInerney JO (2013) Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 30:2263–2267. (PMID: 23883522)
Duan H, Guo J, Xuan L, Wang Z, Li M, Yin Y, Yang Y (2020) Comparative chloroplast genomics of the genus Taxodium. Bmc Genom 21.
Fang J, Hu Y, Hu Z (2024) Comparative analysis of codon usage patterns in 16 Chloroplast genomes of suborder halimedineae. BMC Genomics 25:945. (PMID: 3937980011459826)
Feng Z, Jiang Y, Zheng Y, Miao Y-J, Huang L-F, Luo G-M (2023) Codon use bias analysis of chloroplast genome of Cistanche. Chin Trad Herb Drugs 5, 1540–1550.
Gao Y, Shen G, Yuan G, Tian Z (2022) Comparative analysis of whole chloroplast genomes of three common species of Echinochloa (Gramineae) in paddy fields. Int J Mol Sci 23.
Gilani SS (2025) Aliphatic natural products isolated from Bidens species, the genus Bidens. Springer, pp 129–141.
Guy L, Roat Kultima J, Andersson SG (2010) GenoPlotR: comp gene genome visualization R. Bioinf 26:2334–2335.
Hu Q, Wu JQ, Fan CC, Luo YJ, Liu J, Deng ZJ, Li Q (2024) Comparative analysis of codon usage bias in the chloroplast genomes of eighteen ampelopsideae species (Vitaceae). Bmc Genom Data 25.
Ijaz S, Abbasi BA, Iqbal J, Ullah Z, Yaseen T, Munir M, Kanwal S, Mahmood T, Shah SA, Khan I (2025) Anti-inflammatory and analgesic activity of Bidens species. Chemistry and Pharmacology. Springer, The Genus Bidens, pp 189–203.
Iram S, Hayat MQ, Tahir M, Gul A, Abdullah, Ahmed I (2019) Chloroplast genome sequence of Artemisia scoparia. Comparative analyses and screening of mutational hotspots. Plants-Basel 8.
Jia X, Wei J, Chen Y, Zeng C, Deng C, Zeng P, Tang Y, Zhou Q, Huang Y, Zhu Q (2025) Codon usage patterns and genomic variation analysis of Chloroplast genomes provides new insights into the evolution of aroideae. Sci Rep 15:4333. (PMID: 3991023611799533)
Karimov B, Tojibaev SK, Azimova D, Yusupov Z, Liu L (2025) Comparative analysis of complete Chloroplast genomes of Cousinia (Asteraceae) species. Front Plant Sci 16.
Kato-Noguchi H, Kurniadie D (2024) The invasive mechanisms of the noxious alien plant species Bidens Pilosa. Plants 13:356. (PMID: 3833788910857670)
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. (PMID: 233296903603318)
Kim G-B, Lim CE, Kim J-S, Kim K, Lee JH, Yu H-J, Mun J-H (2020) Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East asia: insights into evolutionary divergence and phylogenomic implications. BMC Genom 21.
Knight RD, Landweber LF (2000) The early evolution of the genetic code. Cell 101:569–572. (PMID: 10892641)
Krämer C, Boehm CR, Liu J, Ting MKY, Hertle AP, Forner J, Ruf S, Schöttler MA, Zoschke R, Bock R (2024) Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number. Nat Plants 10:923–935. (PMID: 3880256111208156)
Lê S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25:1–18.
Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221. (PMID: 3328815)
Li N, Li Y, Zheng C, Huang J, Zhang S (2016) Genome-wide comparative analysis of the codon usage patterns in plants. Genes Genom 38:723–731.
Li F, Zhu J, Liu X, Gao K, Zhao C (2020) The complete chloroplast genome of an invasive herb Bidens frondosa L. (Asteraceae). Mitochondrial DNA Part B-Resour 5: 1769–1770.
Li T, Ma Z, Ding T, Yang Y, Wang F, Wan X, Liang F, Chen X, Yao H (2024) Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species. Funct Integ Genom 24.
Li X, Mo X, Wang D (2025) Phylogeny and evolutionary dynamics of the Rubia genus based on the Chloroplast genome of Rubia Tibetica. Sci Rep 15:14370. (PMID: 4027493212022247)
Lin K, Tan SB, Kolatkar PR, Epstein RJ (2003) Nonrandom intragenic variations in patterns of codon bias implicate a sequential interplay between transitional genetic drift and functional amino acid selection. J Mol Evol 57:538–545. (PMID: 14738312)
Lin Y-X, Duan R-Y, Tan Z-X, Ma Y-H, Wu H (2020) The complete chloroplast genome of the invasive and Cd-hyperaccumulator herb Bidens pilosa L. (Asteraceae). Mitochondrial DNA Part B-Resour 5: 436–438.
Ling L, Zhang S, Yang T (2024) Analysis of codon usage bias in chloroplast genomes of Dryas octopetala var. asiatica (Rosaceae). Genes 15: 899.
Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C (2023) CPGView: a package for visualizing detailed Chloroplast genome structures. Mol Ecol Resour 23:694–704. (PMID: 36587992)
Liu B, Wu H, Cao Y, Ma G, Zheng X, Zhu H, Song X, Sui S (2025) Reducing costs and shortening the cetyltrimethylammonium bromide (CTAB) method to improve DNA extraction efficiency from wintersweet and some other plants. Sci Rep 15:13441–13441. (PMID: 4025124212008413)
Lizarazu MA, Beck SG, Fuentes A, Freire SE (2024) A revision of Bidens (ASTERACEAE: COREOPSIDEAE) from Bolivia1. Ann Mo Bot Gard 109: 163–207.
Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR (2021) Extremely low nucleotide diversity among thirty-six new Chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative Chloroplast genomics analyses with closely related genera. PeerJ 9.
Luo C, Huang W, Sun H, Yer H, Li X, Li Y, Yan B, Wang Q, Wen Y, Huang M (2021) Comparative chloroplast genome analysis of impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. BMC Genom 22:1–18.
Mao H, Wang Z, Shan Y, Cheng X, Yu J (2024) The complete genome sequence of the chloroplast of Bidens aurea. Mitochondrial DNA Part B-Resour 9:1487–1491.
Mudunuri SB, Nagarajaram HA (2007) IMEx: imperfect microsatellite extractor. Bioinformatics 23:1181–1187. (PMID: 17379689)
Nie X, Deng P, Feng K, Liu P, Du X, You FM, Weining S (2014) Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family. Plant Mol Biology Report 32:828–840.
Niu Y, Qin Q, Dong Y, Wang X, Zhang S, Mu Z (2023) Chloroplast genome structure and phylogenetic analysis of 13 lamiaceae plants in Tibet. Front Biosci-Landmark 28:110.
Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Tsegmed Z, Bayarmaa G-A, Lazkov G, Pyak E, Gil H-Y, Park I, Choi HJ (2024) Comparative plastome analysis and taxonomic classification of snow Lotus species (Saussurea, Asteraceae) in central Asia and Southern Siberia. Funct Integr Genom 24:42.
Osaki S, Wasaki J, Nakatsubo T (2022) Phenological shifts of the invasive annual weed Bidens pilosa var. pilosa in response to warmer temperature. Plant Ecol 223:1155–1165.
Parvathy ST, Udayasuriyan V, Bhadana V (2022) Codon usage bias. Mol Biol Rep 49:539–565. (PMID: 34822069)
Pascual-Díaz JP, Garcia S, Vitales D (2021) Plastome diversity and phylogenomic relationships in Asteraceae. Plants 10:2699. (PMID: 349611698705268)
Ping J, Hao J, Wang T, Su Y (2024) Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae. Front Plant Sci 15:1351388. (PMID: 3869392211061511)
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222.
Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
Ren W, Jiang S, Ma L, Kong L, Zhang X, Wu J, Wu W, Liu B, Wang J, Xu J (2025) Full-length Chloroplast genome of vincetoxicum atratum and phylogeny of the genus Vincetoxicum. Genet Resour Crop Evol 72:3719–3731.
Robbins EH, Kelly S (2023) The evolutionary constraints on angiosperm Chloroplast adaptation. Genome Biol Evol 15:evad101. (PMID: 3727950410279810)
Röschenbleck J, Wicke S, Weinl S, Kudla J, Müller KF (2017) Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae). Genome Biol Evol 9:64–76. (PMID: 28172771)
Roth A, Anisimova M, Cannarozzi GM (2012) Measuring codon usage bias. Codon Evol: Mech Models 189–217.
Saboon (2025) Anticancer and antioxidant activities of Bidens species, the genus Bidens: chemistry and pharmacology. Springer, pp 181–188.
Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A (2021) Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. Planta 253.
Sharp PM, Tuohy TM, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143. (PMID: 3526280311530)
Tang D, Wei F, Kashif MH, Khan A, Li Z, Shi Q, Jia R, Xie H, Zhang L, Li B, Chen P, Zhou R (2018) Analysis of Chloroplast differences in leaves of rice isonuclear alloplasmic lines. Protoplasma 255:863–871. (PMID: 29247278)
Tautz D, Schlötterer C (1994) Simple sequences. Curr Opin Genet Dev 4:832–837. (PMID: 7888752)
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:W6–W11. (PMID: 284866355570176)
Wagner WL, Clark JR, Lorence DH (2014) Revision of endemic Marquesas Islands Bidens (Asteraceae, Coreopsideae). PhytoKeys pp 37–67.
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinform 8:77–80.
Wang L, Xing H, Yuan Y, Wang X, Saeed M, Tao J, Feng W, Zhang G, Song X, Sun X (2018) Genome-wide analysis of codon usage bias in four sequenced cotton species. PLoS One 13.
Wang Z-X, Wang D-J, Yi T-S (2022) Does IR-loss promote plastome structural variation and sequence evolution? Front Plant Sci 13:888049. (PMID: 362475679560873)
Wang Y, Zhang C-F, Odago WO, Jiang H, Yang J-X, Hu G-W, Wang Q-F (2023) Evolution of 101 apocynaceae plastomes and phylogenetic implications. Mol Phylogenet Evol 180:107688. (PMID: 36581140)
Wei N, Pérez-Escobar OA, Musili PM, Huang W-C, Yang J-B, Hu A-Q, Hu G-W, Grace OM, Wang Q-F (2021) Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region. Front Plant Sci 12:712064. (PMID: 344219638372406)
Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87:23–29. (PMID: 2110097)
Wu D, Qin Q, Wang X, Niu Y, Zhang S, Mu Z (2023) Sequence analysis of the plastomes of two Tibetan medicinal plants of the family papaveraceae. Front Biosci-Landmark 28:352.
Wu H, Li D-Z, Ma P-F (2024) Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 22:97. (PMID: 3867971811057118)
Xiao M, Hu X, Li Y, Liu Q, Shen S, Jiang T, Zhang L, Zhou Y, Li Y, Luo X (2024) Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes. Physiol Mol Biology Plants 30:153–166.
Xu C, Cai X, Chen Q, Zhou H, Cai Y, Ben A (2011) Factors affecting synonymous codon usage bias in chloroplast genome of Oncidium Gower Ramsey. Evol Bioinform 7: 271–278.
Xu W, Xia B, Li X (2020) The complete Chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses. Sci Rep 10:20782. (PMID: 332471727699626)
Yang Z, Nielsen R (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25:568–579. (PMID: 18178545)
Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C (2023a) Analysis of codon usage patterns in 48 Aconitum species. Bmc Genom 24.
Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL (2023b) Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. Front Plant Sci 14.
Yang X, Wang Y, Gong W, Li Y (2024a) Comparative analysis of the codon usage pattern in the chloroplast genomes of Gnetales species. Int J Mol Sci 25.
Yang Y, Wang X, Shi Z (2024b) Comparative study on codon usage patterns across chloroplast genomes of eighteen Taraxacum Species. Horticulturae 10.
Zhan QB, Huang YL, Xue XM, Chen YX (2024) Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae). Bmc Genom Data 25.
Zhang X, Deng T, Moore MJ, Ji Y, Lin N, Zhang H, Meng A, Wang H, Sun Y, Sun H (2019) Plastome phylogenomics of Saussurea (Asteraceae: cardueae). BMC Plant Biol 19:290. (PMID: 312664656604455)
Zhang D, Tu J, Ding X, Guan W, Gong L, Qiu X, Huang Z, Su H (2023a) Analysis of the chloroplast genome and phylogenetic evolution of Bidens Pilosa. BMC Genom 24.
Zhang Y, Tian L, Lu C (2023b) Chloroplast gene expression: recent advances and perspectives. Plant Commun 4.
Zhu A, Guo W, Gupta S, Fan W, Mower JP (2016) Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol 209:1747–1756. (PMID: 26574731)
Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of Chloroplast genomes. Bioinformatics 34:3030–3031. (PMID: 29659705)
Barbosa ML, Alves M, Roque N (2023aa) Untangling the tribe Coreopsideae (Asteraceae) beyond taxonomic concepts. Acta Bot Brasilica 37.
Barbosa ML, Alves M, Roque N (2023b) Untangling the tribe Coreopsideae (Asteraceae) beyond taxonomic concepts. Acta Bot Brasilica 37:e20230068.
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583–2585. (PMID: 283984595870701)
Benitez-Villasenor A, Mendoza CG, Wanke S, Cevallos MP, Freire ME, Lemmon EM, Lemmon AR, Magallon S (2023) The use of anchored hybrid enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 181:107714. (PMID: 36708940)
Brinkman FS, Leipe DD (2001) Phylogenetic analysis. Bioinformatics: Practical Guide Anal Genes Proteins 2:349.
Camiolo S, Melito S, Porceddu A (2015) New insights into the interplay between codon bias determinants in plants. DNA Res 22:461–469. (PMID: 265462254675714)
Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, Chen S (2022) Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan plateau. BMC Plant Biol 22:195. (PMID: 354137909004202)
Cao Z, Yang L, Xin Y, Xu W, Li Q, Zhang H, Tu Y, Song Y, Xin P (2023) Comparative and phylogenetic analysis of complete Chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). Front Plant Sci 14:1205051. (PMID: 3748447610362447)
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. (PMID: 195059452712344)
Cauz-Santos LA (2025) Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms. New Phytologist.
Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC (2020) A repertory of rearrangements and the loss of an inverted repeat region in Passiflora Chloroplast genomes. Genome Biol Evol 12:1841–1857. (PMID: 327227487586853)
Chauhan BS, Ali HH, Florentine S (2019) Seed germination ecology of Bidens Pilosa and its implications for weed management. Sci Rep 9:16004. (PMID: 316908896831588)
Chetri BK, Senapati A, Sonu S, Shelke RG, Mitra S, Rangan L (2025) Comparative plastome analysis of apocynaceae with de Novo sequencing of Thevetia peruviana: insights into evolution and phylogeny. Trop Plant Biology 18:1–14.
Chiang YM, Chuang DY, Wang SY, Kuo YH, Tsai PW, Shyur LF (2004) Metabolite profiling and chemopreventive bioactivity of plant extracts from < i >Bidens Pilosa. J Ethnopharmacol 95:409–419. (PMID: 15507368)
Daniell H, Lin C-S, Yu M, Chang W-J (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17.
Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45.
Dobrogojski J, Adamiec M, Lucinski R (2020) The Chloroplast genome: a review. Acta Physiol Plant 42.
Doherty A, McInerney JO (2013) Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 30:2263–2267. (PMID: 23883522)
Duan H, Guo J, Xuan L, Wang Z, Li M, Yin Y, Yang Y (2020) Comparative chloroplast genomics of the genus Taxodium. Bmc Genom 21.
Fang J, Hu Y, Hu Z (2024) Comparative analysis of codon usage patterns in 16 Chloroplast genomes of suborder halimedineae. BMC Genomics 25:945. (PMID: 3937980011459826)
Feng Z, Jiang Y, Zheng Y, Miao Y-J, Huang L-F, Luo G-M (2023) Codon use bias analysis of chloroplast genome of Cistanche. Chin Trad Herb Drugs 5, 1540–1550.
Gao Y, Shen G, Yuan G, Tian Z (2022) Comparative analysis of whole chloroplast genomes of three common species of Echinochloa (Gramineae) in paddy fields. Int J Mol Sci 23.
Gilani SS (2025) Aliphatic natural products isolated from Bidens species, the genus Bidens. Springer, pp 129–141.
Guy L, Roat Kultima J, Andersson SG (2010) GenoPlotR: comp gene genome visualization R. Bioinf 26:2334–2335.
Hu Q, Wu JQ, Fan CC, Luo YJ, Liu J, Deng ZJ, Li Q (2024) Comparative analysis of codon usage bias in the chloroplast genomes of eighteen ampelopsideae species (Vitaceae). Bmc Genom Data 25.
Ijaz S, Abbasi BA, Iqbal J, Ullah Z, Yaseen T, Munir M, Kanwal S, Mahmood T, Shah SA, Khan I (2025) Anti-inflammatory and analgesic activity of Bidens species. Chemistry and Pharmacology. Springer, The Genus Bidens, pp 189–203.
Iram S, Hayat MQ, Tahir M, Gul A, Abdullah, Ahmed I (2019) Chloroplast genome sequence of Artemisia scoparia. Comparative analyses and screening of mutational hotspots. Plants-Basel 8.
Jia X, Wei J, Chen Y, Zeng C, Deng C, Zeng P, Tang Y, Zhou Q, Huang Y, Zhu Q (2025) Codon usage patterns and genomic variation analysis of Chloroplast genomes provides new insights into the evolution of aroideae. Sci Rep 15:4333. (PMID: 3991023611799533)
Karimov B, Tojibaev SK, Azimova D, Yusupov Z, Liu L (2025) Comparative analysis of complete Chloroplast genomes of Cousinia (Asteraceae) species. Front Plant Sci 16.
Kato-Noguchi H, Kurniadie D (2024) The invasive mechanisms of the noxious alien plant species Bidens Pilosa. Plants 13:356. (PMID: 3833788910857670)
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. (PMID: 233296903603318)
Kim G-B, Lim CE, Kim J-S, Kim K, Lee JH, Yu H-J, Mun J-H (2020) Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East asia: insights into evolutionary divergence and phylogenomic implications. BMC Genom 21.
Knight RD, Landweber LF (2000) The early evolution of the genetic code. Cell 101:569–572. (PMID: 10892641)
Krämer C, Boehm CR, Liu J, Ting MKY, Hertle AP, Forner J, Ruf S, Schöttler MA, Zoschke R, Bock R (2024) Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number. Nat Plants 10:923–935. (PMID: 3880256111208156)
Lê S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25:1–18.
Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221. (PMID: 3328815)
Li N, Li Y, Zheng C, Huang J, Zhang S (2016) Genome-wide comparative analysis of the codon usage patterns in plants. Genes Genom 38:723–731.
Li F, Zhu J, Liu X, Gao K, Zhao C (2020) The complete chloroplast genome of an invasive herb Bidens frondosa L. (Asteraceae). Mitochondrial DNA Part B-Resour 5: 1769–1770.
Li T, Ma Z, Ding T, Yang Y, Wang F, Wan X, Liang F, Chen X, Yao H (2024) Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species. Funct Integ Genom 24.
Li X, Mo X, Wang D (2025) Phylogeny and evolutionary dynamics of the Rubia genus based on the Chloroplast genome of Rubia Tibetica. Sci Rep 15:14370. (PMID: 4027493212022247)
Lin K, Tan SB, Kolatkar PR, Epstein RJ (2003) Nonrandom intragenic variations in patterns of codon bias implicate a sequential interplay between transitional genetic drift and functional amino acid selection. J Mol Evol 57:538–545. (PMID: 14738312)
Lin Y-X, Duan R-Y, Tan Z-X, Ma Y-H, Wu H (2020) The complete chloroplast genome of the invasive and Cd-hyperaccumulator herb Bidens pilosa L. (Asteraceae). Mitochondrial DNA Part B-Resour 5: 436–438.
Ling L, Zhang S, Yang T (2024) Analysis of codon usage bias in chloroplast genomes of Dryas octopetala var. asiatica (Rosaceae). Genes 15: 899.
Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C (2023) CPGView: a package for visualizing detailed Chloroplast genome structures. Mol Ecol Resour 23:694–704. (PMID: 36587992)
Liu B, Wu H, Cao Y, Ma G, Zheng X, Zhu H, Song X, Sui S (2025) Reducing costs and shortening the cetyltrimethylammonium bromide (CTAB) method to improve DNA extraction efficiency from wintersweet and some other plants. Sci Rep 15:13441–13441. (PMID: 4025124212008413)
Lizarazu MA, Beck SG, Fuentes A, Freire SE (2024) A revision of Bidens (ASTERACEAE: COREOPSIDEAE) from Bolivia1. Ann Mo Bot Gard 109: 163–207.
Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR (2021) Extremely low nucleotide diversity among thirty-six new Chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative Chloroplast genomics analyses with closely related genera. PeerJ 9.
Luo C, Huang W, Sun H, Yer H, Li X, Li Y, Yan B, Wang Q, Wen Y, Huang M (2021) Comparative chloroplast genome analysis of impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. BMC Genom 22:1–18.
Mao H, Wang Z, Shan Y, Cheng X, Yu J (2024) The complete genome sequence of the chloroplast of Bidens aurea. Mitochondrial DNA Part B-Resour 9:1487–1491.
Mudunuri SB, Nagarajaram HA (2007) IMEx: imperfect microsatellite extractor. Bioinformatics 23:1181–1187. (PMID: 17379689)
Nie X, Deng P, Feng K, Liu P, Du X, You FM, Weining S (2014) Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family. Plant Mol Biology Report 32:828–840.
Niu Y, Qin Q, Dong Y, Wang X, Zhang S, Mu Z (2023) Chloroplast genome structure and phylogenetic analysis of 13 lamiaceae plants in Tibet. Front Biosci-Landmark 28:110.
Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Tsegmed Z, Bayarmaa G-A, Lazkov G, Pyak E, Gil H-Y, Park I, Choi HJ (2024) Comparative plastome analysis and taxonomic classification of snow Lotus species (Saussurea, Asteraceae) in central Asia and Southern Siberia. Funct Integr Genom 24:42.
Osaki S, Wasaki J, Nakatsubo T (2022) Phenological shifts of the invasive annual weed Bidens pilosa var. pilosa in response to warmer temperature. Plant Ecol 223:1155–1165.
Parvathy ST, Udayasuriyan V, Bhadana V (2022) Codon usage bias. Mol Biol Rep 49:539–565. (PMID: 34822069)
Pascual-Díaz JP, Garcia S, Vitales D (2021) Plastome diversity and phylogenomic relationships in Asteraceae. Plants 10:2699. (PMID: 349611698705268)
Ping J, Hao J, Wang T, Su Y (2024) Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae. Front Plant Sci 15:1351388. (PMID: 3869392211061511)
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222.
Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
Ren W, Jiang S, Ma L, Kong L, Zhang X, Wu J, Wu W, Liu B, Wang J, Xu J (2025) Full-length Chloroplast genome of vincetoxicum atratum and phylogeny of the genus Vincetoxicum. Genet Resour Crop Evol 72:3719–3731.
Robbins EH, Kelly S (2023) The evolutionary constraints on angiosperm Chloroplast adaptation. Genome Biol Evol 15:evad101. (PMID: 3727950410279810)
Röschenbleck J, Wicke S, Weinl S, Kudla J, Müller KF (2017) Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae). Genome Biol Evol 9:64–76. (PMID: 28172771)
Roth A, Anisimova M, Cannarozzi GM (2012) Measuring codon usage bias. Codon Evol: Mech Models 189–217.
Saboon (2025) Anticancer and antioxidant activities of Bidens species, the genus Bidens: chemistry and pharmacology. Springer, pp 181–188.
Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A (2021) Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. Planta 253.
Sharp PM, Tuohy TM, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143. (PMID: 3526280311530)
Tang D, Wei F, Kashif MH, Khan A, Li Z, Shi Q, Jia R, Xie H, Zhang L, Li B, Chen P, Zhou R (2018) Analysis of Chloroplast differences in leaves of rice isonuclear alloplasmic lines. Protoplasma 255:863–871. (PMID: 29247278)
Tautz D, Schlötterer C (1994) Simple sequences. Curr Opin Genet Dev 4:832–837. (PMID: 7888752)
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:W6–W11. (PMID: 284866355570176)
Wagner WL, Clark JR, Lorence DH (2014) Revision of endemic Marquesas Islands Bidens (Asteraceae, Coreopsideae). PhytoKeys pp 37–67.
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinform 8:77–80.
Wang L, Xing H, Yuan Y, Wang X, Saeed M, Tao J, Feng W, Zhang G, Song X, Sun X (2018) Genome-wide analysis of codon usage bias in four sequenced cotton species. PLoS One 13.
Wang Z-X, Wang D-J, Yi T-S (2022) Does IR-loss promote plastome structural variation and sequence evolution? Front Plant Sci 13:888049. (PMID: 362475679560873)
Wang Y, Zhang C-F, Odago WO, Jiang H, Yang J-X, Hu G-W, Wang Q-F (2023) Evolution of 101 apocynaceae plastomes and phylogenetic implications. Mol Phylogenet Evol 180:107688. (PMID: 36581140)
Wei N, Pérez-Escobar OA, Musili PM, Huang W-C, Yang J-B, Hu A-Q, Hu G-W, Grace OM, Wang Q-F (2021) Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region. Front Plant Sci 12:712064. (PMID: 344219638372406)
Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87:23–29. (PMID: 2110097)
Wu D, Qin Q, Wang X, Niu Y, Zhang S, Mu Z (2023) Sequence analysis of the plastomes of two Tibetan medicinal plants of the family papaveraceae. Front Biosci-Landmark 28:352.
Wu H, Li D-Z, Ma P-F (2024) Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 22:97. (PMID: 3867971811057118)
Xiao M, Hu X, Li Y, Liu Q, Shen S, Jiang T, Zhang L, Zhou Y, Li Y, Luo X (2024) Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes. Physiol Mol Biology Plants 30:153–166.
Xu C, Cai X, Chen Q, Zhou H, Cai Y, Ben A (2011) Factors affecting synonymous codon usage bias in chloroplast genome of Oncidium Gower Ramsey. Evol Bioinform 7: 271–278.
Xu W, Xia B, Li X (2020) The complete Chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses. Sci Rep 10:20782. (PMID: 332471727699626)
Yang Z, Nielsen R (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25:568–579. (PMID: 18178545)
Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C (2023a) Analysis of codon usage patterns in 48 Aconitum species. Bmc Genom 24.
Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL (2023b) Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. Front Plant Sci 14.
Yang X, Wang Y, Gong W, Li Y (2024a) Comparative analysis of the codon usage pattern in the chloroplast genomes of Gnetales species. Int J Mol Sci 25.
Yang Y, Wang X, Shi Z (2024b) Comparative study on codon usage patterns across chloroplast genomes of eighteen Taraxacum Species. Horticulturae 10.
Zhan QB, Huang YL, Xue XM, Chen YX (2024) Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae). Bmc Genom Data 25.
Zhang X, Deng T, Moore MJ, Ji Y, Lin N, Zhang H, Meng A, Wang H, Sun Y, Sun H (2019) Plastome phylogenomics of Saussurea (Asteraceae: cardueae). BMC Plant Biol 19:290. (PMID: 312664656604455)
Zhang D, Tu J, Ding X, Guan W, Gong L, Qiu X, Huang Z, Su H (2023a) Analysis of the chloroplast genome and phylogenetic evolution of Bidens Pilosa. BMC Genom 24.
Zhang Y, Tian L, Lu C (2023b) Chloroplast gene expression: recent advances and perspectives. Plant Commun 4.
Zhu A, Guo W, Gupta S, Fan W, Mower JP (2016) Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol 209:1747–1756. (PMID: 26574731)
Grant Information:
BLX202162 The Fundamental Research Funds for the Central Universities
Contributed Indexing:
Keywords: Bidens; Codon usage bias; Comparative genomics; Evolutionary analysis; Phylogenetic relationships; Plastome; Simple sequence repeats
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20250827 Date Completed: 20250827 Latest Revision: 20250827
Update Code:
20250903
DOI:
10.1007/s10142-025-01699-7
PMID:
40864307
Database:
MEDLINE
Weitere Informationen
Plastome evolution in species-rich angiosperm lineages remains poorly understood despite recent advances in phylogenomics, particularly regarding the mechanistic drivers of codon usage bias (CUB) and their relationship to adaptive evolution. The genus Bidens (Asteraceae), comprising approximately 280 species, represents a morphologically diverse lineage with significant medicinal and economic value. Here, we assembled the complete plastid genome (plastome) of Bidens alba and conducted comprehensive comparative analyses across 31 Bidens species, integrating structural characterization, simple sequence repeat (SSR) distribution, codon usage bias assessment, and selection pressure analysis through Ka/Ks ratios and phylogenomic reconstruction. All plastomes exhibited the canonical angiosperm quadripartite structure (150,490 - 151,856 bp) with consistent AT bias (average GC content: 37.48%) and mononucleotide SSR predominance (37.43%). Twenty-nine high-frequency codons displayed strong AT preference, with multiple analytical approaches confirming natural selection as the primary driver of codon usage bias. The non-synonymous (Ka) /synonymous (Ks) substitution ratios revealed that most protein-coding genes showed evidence of purifying selection (Ka/Ks < 0.5), though the ycf2 and accD genes displayed elevated ratios suggesting adaptive evolution. Phylogenomic reconstruction supported Bidens monophyly with high bootstrap values and resolved species relationships with high confidence. Comparative structural analysis revealed exceptional genomic conservation across the genus, suggesting that while sequence evolution has occurred, the fundamental genomic architecture remains stable. These findings provide crucial insights into significant structural conservation across Bidens plastomes while demonstrating active sequence-level evolution, providing crucial insights into plastome evolutionary mechanisms within rapidly diversifying lineages and establish a robust genomic framework for understanding ecological adaptation and phylogenetic relationships in this ecologically important lineage.
(© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Declarations. Competing interests: The authors declare no competing interests.