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Research Articles

Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine

, , & ORCID Icon
Pages 231-237 | Received 18 May 2022, Accepted 21 Aug 2022, Published online: 05 Sep 2022

References

  • Park MS, Fong JJ, Oh S-Y, et al. Marine-derived Penicillium in Korea: diversity, enzyme activity, and antifungal properties. Antonie Van Leeuwenhoek. 2014;106(2):331–345.
  • Nguyen TT, Pangging M, Bangash NK, et al. Five new records of the family Aspergillaceae in Korea, Aspergillus europaeus, A. pragensis, A. tennesseensis, Penicillium fluviserpens, and P. scabrosum. Mycobiology. 2020;48(2):81–94.
  • He F, Li X, Yu J-H, et al. Secondary metabolites from the mangrove sediment-derived fungus Penicillium pinophilum SCAU037. Fitoterapia. 2019;136:104177.
  • Honary S, Barabadi H, Gharaei-Fathabad E, et al. Green synthesis of copper oxide nanoparticles using Penicillium aurantiogriseum, Penicillium citrinum and Penicillium waksmanii. Dig J Nanomater Bios. 2012;7(3):999–1005.
  • Visagie C, Houbraken J, Frisvad JC, et al. Identification and nomenclature of the genus Penicillium. Stud Mycol. 2014;78:343–371.
  • Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci USA. 2012;109(16):6241–6246.
  • Sayers EW, Cavanaugh M, Clark K, et al. GenBank. Nucleic Acids Res. 2021;49(D1):D92–D96.
  • Meiklejohn KA, Damaso N, Robertson JM. Assessment of BOLD and GenBank–their accuracy and reliability for the identification of biological materials. PLoS One. 2019;14(6):e0217084.
  • Lee YG, Chung K-C, Wi SG, et al. Purification and properties of a chitinase from Penicillium sp. LYG 0704. Protein Expr Purif. 2009;65(2):244–250.
  • Ngan NTT, Quang TH, Kim K-W, et al. Anti-inflammatory effects of secondary metabolites isolated from the marine-derived fungal strain Penicillium sp. SF-5629. Arch Pharm Res. 2017;40(3):328–337.
  • Kim WK, Sang HK, Woo SK, et al. Six species of Penicillium associated with blue mold of grape. Mycobiology. 2007;35(4):180–185.
  • Park MS, Lee S, Lim YW. A new record of four Penicillium species isolated from Agarum clathratum in Korea. J Microbiol. 2017;55(4):237–246.
  • National List of Species of Korea. 2020. National Institute of Biological Resources. [cited 2021-Sep 30]. Available from: http://kbr.go.kr.
  • Lee S, Hong S-B, Kim C-Y. Contribution to the checklist of soil-inhabiting fungi in Korea. Mycobiology. 2003;31(1):9–18.
  • Houbraken J, Kocsubé S, Visagie C, et al. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): an overview of families, genera, subgenera, sections, series and species. Stud Mycol. 2020;95:5–169.
  • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.
  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313.
  • Park J-E, Kim G-Y, Park H-S, et al. Phylogenetic analysis of caterpillar fungi by comparing ITS1-5.8S-ITS2 ribosomal DNA sequences. Mycobiology. 2001;29(3):121–131.
  • Khan SA, Hamayun M, Yoon H, et al. Plant growth promotion and Penicillium citrinum. BMC Microbiol. 2008;8(1):231–210.
  • Kim CS, Park MS, Yu SH. Two species of endophytic Penicillium from Pinus rigida in Korea. Mycobiology. 2008;36(4):222–227.
  • Bae K-S, Hong S-G, Park Y-D, et al. Sequence comparison of mitochondrial small subunit ribosomal DNA in Penicillium. Journal of Microbiology. 2000;38(2):62–65.
  • Lücking R, Aime MC, Robbertse B, et al. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus. 2020;11(1):1–32.
  • Jung PE, Fong JJ, Park MS, et al. Sequence validation for the identification of the white-rot fungi Bjerkandera in public sequence databases. J Microbiol Biotechnol. 2014;24(10):1301–1307.
  • Jargalmaa S, Eimes JA, Park MS, et al. Taxonomic evaluation of selected Ganoderma species and database sequence validation. PeerJ. 2017;5:e3596.
  • Pentinsaari M, Ratnasingham S, Miller SE, et al. BOLD and GenBank revisited–do identification errors arise in the lab or in the sequence libraries? PLoS One. 2020;15(4):e0231814.
  • Buhay JE. “COI-like” sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol. 2009;29(1):96–110.
  • Fietz K, Graves JA, Olsen MT. Control control control: a reassessment and comparison of GenBank and chromatogram mtDNA sequence variation in Baltic grey seals (Halichoerus grypus). PLoS One. 2013;8(8):e72853.
  • Schuler GD, Epstein JA, Ohkawa H, et al. [10] Entrez: molecular biology database and retrieval system. Methods Enzymol. 1996;266:141–162.
  • Aime MC, Miller AN, Aoki T, et al. How to publish a new fungal species, or name, version 3.0. IMA Fungus. 2021;12(1):1–15.
  • Portik DM, Wiens JJ. SuperCRUNCH: a bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. Methods Ecol Evol. 2020;11(6):763–772.
  • Ha TM, Ko W, Lee SJ, et al. Anti-inflammatory effects of curvularin-type metabolites from a marine-derived fungal strain Penicillium sp. SF-5859 in lipopolysaccharide-induced RAW264. 7 Macrophages. Marine Drugs. 2017;15(9):282.
  • Heo I, Hong K, Yang H, et al. Diversity of Aspergillus, Penicillium, and Talaromyces species isolated from freshwater environments in Korea. Mycobiology. 2019;47(1):12–19.
  • Oh J-Y, Kim E-N, Ryoo M-I, et al. Morphological and molecular identification of Penicillium islandicum isolate KU101 from stored rice. Plant Pathol J. 2008;24(4):469–473.
  • Kim KY, Kim CN. Airborne microbiological characteristics in public buildings of Korea. Build Environ. 2007;42(5):2188–2196.
  • Park MS, Fong JJ, Oh S-Y, et al. Penicillium jejuense sp. nov., isolated from the marine environments of Jeju Island, Korea. Mycologia. 2015;107(1):209–216.
  • Park MS, Lee EJ, Fong JJ, et al. A new record of Penicillium antarcticum from marine environments in Korea. Mycobiology. 2014;42(2):109–113.