636
Views
1
CrossRef citations to date
0
Altmetric
Plastome Report

The complete chloroplast genome and phylogenetic analysis of Jacobaea maritima (Asteraceae)

&
Pages 771-776 | Received 13 Mar 2023, Accepted 15 Jul 2023, Published online: 22 Jul 2023

References

  • Amiryousefi A, Hyvönen J, Poczai P. 2018. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 34(17):3030–3031. doi:10.1093/bioinformatics/bty220.
  • Beier S, Thiel T, Münch T, Scholz U, Mascher M., 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics. 33(16):2583–2585. doi:10.1093/bioinformatics/btx198.
  • Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. doi:10.1093/nar/gkw955.
  • Galasso G, Bartolucci F. 2015. Four new combinations in Jacobaea Mill. (Asteraceae, Senecioneae) for the European flora. Nat Hist Sci. 2(2):95–96. doi:10.4081/nhs.2015.246.
  • Górniak M, Paun O, Chase MW. 2010. Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: congruence with organellar and nuclear ribosomal DNA results. Mol Phylogenet Evol. 56(2):784–795. doi:10.1016/j.ympev.2010.03.003.
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS., 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589. doi:10.1038/nmeth.4285.
  • 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.
  • Krawczyk K, Nobis M, Myszczyński K, Klichowska E, Sawicki J., 2018. Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: stipa). Sci Rep. 8(1):1924. doi:10.1038/s41598-018-20399-w.
  • Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29(22):4633–4642. doi:10.1093/nar/29.22.4633.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R., 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16):2078–2079. doi:10.1093/bioinformatics/btp352.
  • Li J, Tang J, Zeng S, Han F, Yuan J, Yu J., 2021. Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. BMC Plant Biol. 21(1):25. doi:10.1186/s12870-020-02793-7.
  • 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.
  • Maggio A, Venditti A, Senatore F, Bruno M, Formisano C., 2015. Chemical composition of the essential oil of Jacobaea maritima (L.) Pelser & Meijden and Jacobaea maritima subsp. bicolor (Willd.) B. Nord. & Greuter (Asteraceae) collected wild in Croatia and Sicily, respectively. Nat Prod Res. 29(9):857–863. doi:10.1080/14786419.2014.991928.
  • Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A., 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 14(1):e1005944. doi:10.1371/journal.pcbi.1005944.
  • Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. doi:10.1093/molbev/msu300.
  • Passalacqua NG, Peruzzi L, Pellegrino G. 2008. A biosystematic study of the Jacobaea maritima group (Asteraceae, Senecioneae) in the Central Mediterranean area. Taxon. 57(3):893–906. doi:10.1002/tax.573018.
  • Pelser PB, Gravendeel B, van der Meijden R. 2002. Tackling speciose genera: species composition and phylogenetic position of Senecio sect. Jacobaea (Asteraceae) based onplastid and nrDNA sequences. Am J Bot. 89(6):929–939. doi:10.3732/ajb.89.6.929.
  • Pelser PB, Gravendeel B, van der Meijden R. 2003. Phylogeny reconstruction in the gap between too little and too much divergence: the closest relatives of Senecio jacobaea (Asteraceae) according to DNA sequences and AFLPs. Mol Phylogenet Evol. 29(3):613–628. doi:10.1016/s1055-7903(03)00139-8.
  • Qu X-J, Moore MJ, Li D-Z, Yi T-S., 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.
  • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26(6):841–842. doi:10.1093/bioinformatics/btq033.
  • Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C., 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi:10.1093/nar/gkz345.
  • Zhang C, Huang C-H, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H., 2021. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. J Integr Plant Biol. 63(7):1273–1293. doi:10.1111/jipb.13078.
  • Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT., 2020. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355. doi:10.1111/1755-0998.13096.