294
Views
0
CrossRef citations to date
0
Altmetric
Plastome Announcement

The complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890 (Chloranthaceae)

, , , , &
Pages 1224-1228 | Received 09 Aug 2023, Accepted 29 Oct 2023, Published online: 10 Nov 2023

References

  • Cai ZQ, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol. 6(1):77. doi:10.1186/1471-2148-6-77.
  • Chen SF, Zhou YQ, Chen YR, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890. doi:10.1093/bioinformatics/bty560.
  • Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. Gigascience. 10(2):giab008. doi:10.1093/gigascience/giab008.
  • Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
  • Friis EM, Crane PR, Pedersen KR. 1986. Floral evidence for Cretaceous chloranthoid angiosperms. Nature. 320(6058):163–164. doi:10.1038/320163a0.
  • Goremykin V, Hirsch-Ernst KI, Wölfl S, Hellwig FH. 2003. The chloroplast genome of the “basal” angiosperm Calycanthus fertilis – structural and phylogenetic analyses. Plant Syst Evol. 242(1-4):119–135. doi:10.1007/s00606-003-0056-4.
  • Hansen DR, Dastidar SG, Cai ZQ, Penaflor C, Kuehl JV, Boore JL, Jansen RK. 2007. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol. 45(2):547–563. doi:10.1016/j.ympev.2007.06.004.
  • He LH, Zhao XL, Yu J, Zhang Z. 2022. Chloranthus coccineus (Chloranthaceae), a new species from Hubei, China. Phytotaxa. 566(3):279–289. doi:10.11646/phytotaxa.566.3.3.
  • Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. 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.
  • Kang JS, Kim BY, Yoo KO. 2022. The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae. Mitochondrial DNA B Resour. 7(10):1829–1833. doi:10.1080/23802359.2022.2132840.
  • 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.
  • Kong HZ, Chen ZD. 2000. Phylogeny in Chloranthus Swartz (Chloranthaceae) inferred from sequence analysis of nrDNA ITS region. Acta Bot Sin. 42(7):762–764.
  • Kong HZ, Chen ZD, Lu AM. 2002. Phylogeny of Chloranthus (Chloranthaceae) based on nuclear ribosomal ITS and plastid trnL-F sequence data. Am J Bot. 89(6):940–946. doi:10.3732/ajb.89.6.940.
  • Kong HZ. 2000. Systematics of the genus Chloranthus Swartz (Chloranthaceae) [PhD dissertation]. Beijing: Institute of Botany, Chinese Academy of Sciences.
  • Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: 1303.3997v1302 [q-bio.GN].
  • Liu DT, Cai L, Chen G. 2019. Chloranthus flavus (Chloranthaceae), a new species from Guangxi, China. Phytotaxa. 391(4):273–276. doi:10.11646/phytotaxa.391.4.6.
  • Liu XD, Liao XY, Liu ZJ, Lan SR. 2019. Complete chloroplast genome of Chloranthus henryi (Chloranthaceae). Mitochondrial DNA B Resour. 4(2):2964–2965. doi:10.1080/23802359.2019.1637793.
  • Liu SY, Ni Y, Li JJ, Zhang XY, Yang HY, Chen HM, 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.
  • Lu YB, Jiang YL, Qin XM, Zhang Q. 2020. Morphological diversity and geographical distribution of Chloranthus in China. Guihaia. 40(1):31–43.
  • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 37(5):1530–1534. doi:10.1093/molbev/msaa015.
  • Moore MJ, Bell CD, Soltis PS, Soltis DE. 2007. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA. 104(49):19363–19368. doi:10.1073/pnas.0708072104.
  • Shi LC, Chen HM, Jiang M, Wang LQ, Wu X, Huang LF, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi:10.1093/nar/gkz345.
  • Sun J, Zhang G, Li YM, Chen Y, Zhang XF, Tang ZS, Wu HF. 2016. The complete chloroplast genome sequence of Chloranthus japonicus. Mitochondrial DNA A DNA Mapp Seq Anal. 27(5):3202–3204. doi:10.3109/19401736.2015.1007347.
  • Wang W, Zou PS, Liu GF, Dai SP. 2020. Characterization of the complete chloroplast genome sequence of Sarcandra glabra (Chloranthales). Mitochondrial DNA B Resour. 5(1):864–865. doi:10.1080/23802359.2020.1715858.
  • Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB. 2018. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods. 14(1):43. doi:10.1186/s13007-018-0300-0.
  • Zhang Q, Antonelli A, Feild TS, Kong HZ. 2011. Revisiting taxonomy, morphological evolution, and fossil calibration strategies in Chloranthaceae. J Syst Evol. 49(4):315–329. doi:10.1111/j.1759-6831.2011.00129.x.
  • Zhang Q, Feild TS, Antonelli A. 2015. Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity. Am J Bot. 102(4):566–580. doi:10.3732/ajb.1400527.