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Plastome Report

Characterization and phylogenetic analysis of the chloroplast genome of Duhaldea cappa (Buch.-Ham. ex D.Don) Pruski & Anderb. (Asteraceae)

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Pages 186-190 | Received 23 Jul 2023, Accepted 11 Jan 2024, Published online: 25 Jan 2024

References

  • Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. 2006. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc. 1(5):2320–2325. doi:10.1038/nprot.2006.384.
  • Anderberg A. 2005. Evolutionary relationships in the Asteraceae tribe Inuleae (incl. Plucheeae) evidenced by DNA sequences of ndhF; with notes on the systematic positions of some aberrant genera. Org. Divers. Evol. 5(2):135–146. doi:10.1016/j.ode.2004.10.015.
  • Anderberg AA. 1989. Phylogeny and reclassification of the tribe Inuleae (Asteraceae). Can J Bot. 67(8):2277–2296. doi:10.1139/b89-292.
  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. doi:10.1089/cmb.2012.0021.
  • Chen YS, Anderberg AA. 2011. Inuleae. In: wu ZY, Raven PH, Hong DY, editors. Flora of China. Vol. 20–21. Beijing/St. Louis: Science Press/Missouri Botanical Garden Press; p. 844.
  • Chen X, Zhou J, Cui Y, Wang Y, Duan B, Yao H. 2018. Identification of Ligularia herbs using the complete chloroplast genome as a super-barcode. Front Pharmacol. 9:695. doi:10.3389/fphar.2018.00695.
  • Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin-A-Woeng T, Vrieling K. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. 18(2):93–105. doi:10.1093/dnares/dsr002.
  • Downie SR, Jansen RK. 2015. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Syst. Bot. 40(1):336–351. doi:10.1600/036364415X686620.
  • Englund M, Pornpongrungrueng P, Gustafsson MHG, Anderberg AA. 2009. Phylogenetic relationships and generic delimitation in Inuleae subtribe Inulinae (Asteraceae) based on ITS and cpDNA sequence data. Cladistics. 25(4):319–352. doi:10.1111/j.1096-0031.2009.00256.x.
  • Hereward JP, Werth JA, Thornby DF, Keenan M, Chauhan BS, Walter GH. 2018. Complete chloroplast genome of glyphosate resistant Sonchus oleraceus L. from Australia, with notes on the small single copy (SSC) region orientation. Mitochondrial DNA B Resour. 3(1):363–364. doi:10.1080/23802359.2018.1450682.
  • Huang L, Wang Z, Wang T, Su YJ. 2016. The complete chloroplast genome sequence of Mikania micrantha (Asteraceae), a noxious invasive weed to South China. Mitochondrial DNA B Resour. 1(1):603–604. doi:10.1080/23802359.2016.1209090.
  • Kalola J, Shah R, Patel A, Lahiri SK, Shah MB. 2017. Anti-inflammatory and immunomodulatory activities of Inula cappa roots (Compositae). J. Complement Integr. Med. 14(3):20160083. doi:10.1515/jcim-2016-0083.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi:10.1093/molbev/mst010.
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. doi:10.1093/bioinformatics/bts199.
  • Kim G, Lim CE, Kim JS, Kim K, Lee JH, Yu HJ, Mun JH. 2020. Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications. BMC Genomics. 21(1):415. doi:10.1186/s12864-020-06812-7.
  • Li R, Ma PF, Wen J, Yi TS. 2013. Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications. PLoS One. 8(10):e78568. doi:10.1371/journal.pone.0078568.
  • 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(3):694–704. doi:10.1111/1755-0998.13729.
  • Nylinder S, Anderberg AA. 2015. Phylogeny of the Inuleae (Asteraceae) with special emphasis on the Inuleae-Plucheinae. Taxon. 64(1):110–130. doi:10.12705/641.22.
  • Pruski JF, Anderberg AA. 2003. Duhaldea cappa (Buch.-Ham. ex D. Don) Pruski & Anderberg (Compositae: Inuleae), a nomenclatural correction. Comp. Newsl. 40:43–46.
  • Qu XJ, Moore MJ, Li DZ, Yi TS. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15(1):50. doi:10.1186/s13007-019-0435-7.
  • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57(5):758–771. doi:10.1080/10635150802429642.
  • Vargas OM, Ortiz EM, Simpson BB. 2017. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). New Phytol. 214(4):1736–1750. doi:10.1111/nph.14530.
  • Wang A, Wu H, Zhu X, Lin J. 2018. Species identification of Conyza bonariensis assisted by chloroplast genome sequencing. Front Genet. 9:374. doi:10.3389/fgene.2018.00374.
  • Wang B, Zhao Q, Wang XH, Fu ZX. 2020. The complete chloroplast genome of Pertya phylicoides (Asteraceae, Pertyeae): a shurby endemic species from China. Mitochondrial DNA B Resour. 5(1):963–964. doi:10.1080/23802359.2020.1722763.
  • Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352. doi:10.1093/bioinformatics/btv383.
  • Yun SA, Gil HY, Kim SC. 2017. The complete chloroplast genome sequence of Saussurea polylepis (Asteraceae), a vulnerable endemic species of Korea. Mitochondrial DNA B Resour. 2(2):650–651. doi:10.1080/23802359.2017.1375881.
  • Zhang Y, Zhang J, Yang Y, Liu Q. 2017. Complete chloroplast genome of Pluchea indica (L.) Less. (Asteraceae) and its phylogenetic analysis. Mitochondrial DNA B Resour. 2(2):918–919. doi:10.1080/23802359.2017.1413299.
  • Zheng L, Hao X, Yuan C, Huang L, Zhang J, Dong F, Fan T, Wu G, Chen Y, Ma Y, et al. 2015. Study on chemical constituents of Inula cappa. China J. Chin. Mater. Med. 40(4):672–678.