248
Views
0
CrossRef citations to date
0
Altmetric
Plastome Announcement

The complete chloroplast genome of Polygala subopposita, an endemic milkwort in China

Pages 1290-1293 | Received 15 May 2023, Accepted 12 Nov 2023, Published online: 22 Nov 2023

References

  • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17(4):540–552. doi:10.1093/oxfordjournals.molbev.a026334.
  • Chen S-K, Ma H-Y, Parnell JAN, PH, Hong D-Y. 2008. Polygalaceae. In Wu Z-Y, Raven, editors. Flora of China. Beijing & St. Louis: Science Press & Missouri Botanical Garden Press, p. 139–159.
  • Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. doi:10.1186/s13059-020-02154-5.
  • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9(4):357–359. doi:10.1038/nmeth.1923.
  • Lee D-H, Cho W-B, Park BJ, Kim JD, Byeon JG. 2020. The complete chloroplast genome of Polygala tenuifolia, a critically endangered species in Korea. Mitochondrial DNA Part B. 5(2):1919–1920. doi:10.1080/23802359.2020.1754947.
  • 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.
  • Pastore JF, Abbott J, Neubig K, van den Berg C, Mota M, Cabral A, Whitten W. 2019. Phylogeny and biogeography of Polygala (Polygalaceae). Taxon. 68(4):673–691. doi:10.1002/tax.12119.
  • Petersen G, Darby H, Lam VKY, Pedersen HAE, Merckx V, Zervas A, Seberg O, Graham SW. 2019. Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes. Ann Bot. 124(5):791–807. doi:10.1093/aob/mcz114.
  • 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.
  • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577. doi:10.1080/10635150701472164.
  • Wang Y-H, Qu X-J, Chen S-Y, Li D-Z, Yi T-S. 2017a. Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication. Tree Genet Genom. 13:41.
  • Wang Y-H, Wang H, Yi T-S, Wang Y-H. 2017b. The complete chloroplast genomes of Adenolobus garipensis and Cercis glabra (Cercidoideae, Fabaceae). Conservation Genet Resour. 9(4):635–638. doi:10.1007/s12686-017-0744-y.
  • Weng M-L, Blazier JC, Govindu M, Jansen RK. 2014. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol. 31(3):645–659. doi:10.1093/molbev/mst257.
  • Zhang Y-J, Du L-W, Liu A, Chen J-J, Wu L, Hu W-M, Zhang W, Kim K, Lee S-C, Yang T-J, et al. 2016. The complete chloroplast genome sequences of five Epimedium species: lights into phylogenetic and taxonomic analyses. Front Plant Sci. 7:306. doi:10.3389/fpls.2016.00306.
  • Zhang R, Wang Y-H, Jin J-J, Stull GW, Bruneau A, Cardoso D, de Queiroz LP, Moore MJ, Zhang S-D, Chen S-Y, et al. 2020. Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Syst Biol. 69(4):613–622.