843
Views
0
CrossRef citations to date
0
Altmetric
Plastome Announcement

The complete chloroplast genome of Vaccinium oxycoccos (Ericaceae)

, , , &
Pages 942-947 | Received 09 Jun 2023, Accepted 23 Aug 2023, Published online: 04 Sep 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.
  • An R, Niu M, Lou X, Huang H, Lin E., 2022. The complete chloroplast genome of Rhododendron huadingense (Ericaceae). Mitochondrial DNA Part B Resour. 7(11):1910–1912. doi: 10.1080/23802359.2022.2135403.
  • 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.
  • Chen X, Liu Q, Guo W, Wei H, Wang J, Zhu D, Tan Y., 2019. The complete chloroplast genome of Vaccinium duclouxii, an endemic species in China. Mitochondrial DNA Part B Resour. 4(2):2215–2216. doi: 10.1080/23802359.2019.1624644.
  • Cho W-B, Han E-K, Choi I-S, Son DC, Chung GY, Lee J-H., 2021. The complete plastid genome sequence of Vaccinium japonicum (Ericales: Ericaceae), a deciduous broad-leaved shrub endemic to East Asia. Mitochondrial DNA Part B Resour. 6(7):1926–1928. doi: 10.1080/23802359.2021.1935351.
  • Daniell H, Jin S, Zhu X-G, Gitzendanner MA, Soltis DE, Soltis PS., 2021. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. Plant Biotechnol J. 19(3):430–447. doi: 10.1111/pbi.13556.
  • Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissues. Phytochem Bull. 19:11–15.
  • Ermis E, Hertel C, Schneider C, Carle R, Stintzing F, Schmidt H., 2015. Characterization of in vitro antifungal activities of small and American cranberry (Vaccinium oxycoccos L. and V. macrocarpon Aiton) and lingonberry (Vaccinium vitis-idaea L.) concentrates in sugar reduced fruit spreads. Int J Food Microbiol. 204:111–117. doi: 10.1016/j.ijfoodmicro.2015.03.017.
  • Fahrenkrog AM, Matsumoto GO, Toth K, Jokipii-Lukkari S, Salo HM, Häggman H, Benevenuto J, Munoz PR., 2022. Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops. Sci Rep. 12(1):21600. doi: 10.1038/s41598-022-25434-5.
  • Fajardo D, Senalik D, Ames M, Zhu H, Steffan SA, Harbut R, Polashock J, Vorsa N, Gillespie E, Kron K, et al. 2013. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing. Tree Genet Genomes. 9(2):489–498. doi: 10.1007/s11295-012-0573-9.
  • Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I., 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32(Web Server issue):W273–279. doi: 10.1093/nar/gkh458.
  • 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.
  • 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.
  • Guo W, Luo L, Huang Y, Li G, Wang X, Cheng T, Sun Z, Wang F, Zhang L, Li W, et al. 2019. The complete chloroplast genome of Vaccinium fragile (Vacciniaceae), a shrub endemic to China. Mitochondrial DNA Part B Resour. 4(2):2310–2311. doi: 10.1080/23802359.2019.1627948.
  • Hancock JF, Lyrene P, Finn CE, et al. 2008. Blueberries and Cranberries. In: Hancock, J.F. (Ed.), Temperate FRUIT crop breeding: Germplasm to genomics. Dordrecht: Springer Netherlands. Chapter 4:115–150.
  • 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.
  • Jurikova T, Skrovankova S, Mlcek J, Balla S, Snopek L. 2018. Bioactive compounds, antioxidant activity, and biological effects of European Cranberry (Vaccinium oxycoccos). Molecules. 24(1):24. doi: 10.3390/molecules24010024.
  • 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.
  • Kim S-C, Baek S-H, Lee J-W, Hyun HJ., 2019. Complete chloroplast genome of Vaccinium oldhamii and phylogenetic analysis. Mitochondrial DNA. Part B Resources. 4(1):902–903. doi: 10.1080/23802359.2019.1579067.
  • Kim Y, Shin J, Oh D-R, Kim D-W, Lee H-S, Choi C., 2020. Complete chloroplast genome sequences of Vaccinium bracteatum Thunb., V. vitis-idaea L., and V. uliginosum L. (Ericaceae). Mitochondrial DNA. Part B Resources. 5(2):1843–1844. doi: 10.1080/23802359.2020.1750318.
  • 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.
  • Kron KA, Powell EA, Luteyn JL. 2002. Phylogenetic relationships within the blueberry tribe (Vaccinieae, Ericaceae) based on sequence data from MATK and nuclear ribosomal ITS regions, with comments on the placement of Satyria. Am J Bot. 89(2):327–336. doi: 10.3732/ajb.89.2.327.
  • 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., 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.
  • 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.
  • Powell EA, Kathleen AK. 2002. Hawaiian blueberries and their relatives—A phylogenetic analysis of Vaccinium sections Macropelma, Myrtillus, and Hemimyrtillus (Ericaceae). Systematic Botany. 27(4):768–779.
  • 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.
  • Schlautman B, Covarrubias-Pazaran G, Fajardo D, Steffan S, Zalapa J. 2017. Discriminating power of microsatellites in cranberry organelles for taxonomic studies in Vaccinium and Ericaceae. Genet Resour Crop Evol. 64(3):451–466., doi: 10.1007/s10722-016-0371-6.
  • 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.
  • Sleumer H. 1941. Vaccinioidee-Studien. Botanische Jahrbücher. 71:432–433.
  • Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S., 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. doi: 10.1093/nar/gkx391.
  • 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.