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Plastome Report

The complete chloroplast genome sequence of Prunus salicina cultivar ‘Zuili’ (Rosaceae)

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Pages 277-280 | Received 30 Oct 2023, Accepted 05 Feb 2024, Published online: 12 Feb 2024

References

  • Bao W, Ao D, Wuyun T, Li T, Wang L, Liu H. 2019. The complete chloroplast genome of Prunus mira koehne (Prunoideae, Rosaceae), a wild and indigenous peach on Tibet, China. Mitochondrial DNA B Resour. 4(2):3731–3733. doi:10.1080/23802359.2019.1679048.
  • Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890. doi:10.1093/bioinformatics/bty560.
  • Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
  • Geng W, Ouyang L, Xu M, Jing J. 2020. The complete chloroplast genome of Prunus domestica L. (Rosaceae) and its phylogenetic implication. Mitochondrial DNA B Resour. 5(3):2783–2784. doi:10.1080/23802359.2020.1768928.
  • Greiner S, Lehwark P, Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 47(W1):W59–W64. doi:10.1093/nar/gkz238.
  • Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H. 2011. Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol. 28(1):835–847. doi:10.1093/molbev/msq261.
  • Jia HJ, Yang X, He FJ, Li B. 2013. Anatomical studies of ovule development in the post-bloom pistils of the “Zuili” plum (Prunus salicina Lindl.). J Zhejiang Univ Sci B. 14(9):800–806.
  • Jiang D, Liu X, Shen X. 2019. The complete chloroplast genome of Prunus verecunda, and phylogenetic analysis with Amygdaleae species. Mitochondrial DNA B Resour. 4(2):3338–3339. doi:10.1080/23802359.2019.1673228.
  • 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.
  • 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.
  • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14):1754–1760. doi:10.1093/bioinformatics/btp324.
  • 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.
  • Liu J, Yin R, Xu Z, Tian Y. 2019. The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China. Mitochondrial DNA B Resour. 4(2):3383–3385. doi:10.1080/23802359.2019.1673236.
  • 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.
  • Mu J, Zhao Y, He Y, Sun J, Yuan Q. 2021. The complete chloroplast genome of Prunus japonica thunb. (Rosaceae), an ornamental and medicinal plant. Mitochondrial DNA B Resour. 6(1):112–114. doi:10.1080/23802359.2020.1848477.
  • Nguyen LT, 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.
  • 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.
  • Su N, Hodel RGJ, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, et al. 2023. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. Plant Divers. 45(4):397–408. doi:10.1016/j.pld.2023.03.013.
  • Zhang X, Yan J, Ling Q, Fan L, Zhang M. 2018. Complete chloroplast genome sequence of Prunus davidiana (Rosaceae). Mitochondrial DNA B Resour. 3(2):888–889. doi:10.1080/23802359.2018.1501325.