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http://dx.doi.org/10.1080/12298093.2022.2116816

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

Chang Wan Seo (School of Biological Sciences, and Institute of Microbiology, Seoul National University)
Sung Hyun Kim (School of Biological Sciences, and Institute of Microbiology, Seoul National University)
Young Woon Lim (School of Biological Sciences, and Institute of Microbiology, Seoul National University)
Myung Soo Park (Department of Crops and Forestry, Korea National University of Agriculture and Fisheries)
Publication Information
Mycobiology / v.50, no.4, 2022 , pp. 231-237 More about this Journal
Abstract
Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, b-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium reidentification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.
Keywords
GenBank; inventory; Penicillium; re-identification; tree-based identification;
Citations & Related Records
Times Cited By KSCI : 11  (Citation Analysis)
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1 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.   DOI
2 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.   DOI
3 He F, Li X, Yu J-H, et al. Secondary metabolites from the mangrove sediment-derived fungus Penicillium pinophilum SCAU037. Fitoterapia. 2019;136:104177.
4 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.
5 Visagie C, Houbraken J, Frisvad JC, et al. Identification and nomenclature of the genus Penicillium. Stud Mycol. 2014;78:343-371.   DOI
6 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.   DOI
7 Sayers EW, Cavanaugh M, Clark K, et al. GenBank. Nucleic Acids Res. 2021;49(D1):D92-D96.   DOI
8 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.
9 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.   DOI
10 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.   DOI
11 Kim WK, Sang HK, Woo SK, et al. Six species of Penicillium associated with blue mold of grape. Mycobiology. 2007;35(4):180-185.   DOI
12 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.   DOI
13 National List of Species of Korea. 2020. National Institute of Biological Resources. [cited 2021-Sep 30]. Available from: http://kbr.go.kr.
14 Lee S, Hong S-B, Kim C-Y. Contribution to the checklist of soil-inhabiting fungi in Korea. Mycobiology. 2003;31(1):9-18.   DOI
15 Houbraken J, Kocsub e 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.   DOI
16 Khan SA, Hamayun M, Yoon H, et al. Plant growth promotion and Penicillium citrinum. BMC Microbiol. 2008;8(1):231-210.
17 Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-780.   DOI
18 Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312-1313.   DOI
19 Park J-E, Kim G-Y, Park H-S, et al. Phylogenetic analysis of caterpillar fungi by comparing ITS1-5.8SITS2 ribosomal DNA sequences. Mycobiology. 2001;29(3):121-131.   DOI
20 Kim CS, Park MS, Yu SH. Two species of endophytic Penicillium from Pinus rigida in Korea. Mycobiology. 2008;36(4):222-227.   DOI
21 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.
22 Lucking 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.   DOI
23 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.   DOI
24 Jargalmaa S, Eimes JA, Park MS, et al. Taxonomic evaluation of selected Ganoderma species and database sequence validation. PeerJ. 2017;5:e3596.
25 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.
26 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.   DOI
27 Buhay JE. "COI-like" sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol. 2009;29(1):96-110.   DOI
28 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.
29 Schuler GD, Epstein JA, Ohkawa H, et al. [10] Entrez: molecular biology database and retrieval system. Methods Enzymol. 1996;266:141-162.   DOI
30 Portik DM, Wiens JJ. SuperCRUNCH: a bioinformatics toolkit for creating and manipulating super-matrices and other large phylogenetic datasets. Methods Ecol Evol. 2020;11(6):763-772.   DOI
31 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.
32 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.   DOI
33 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.   DOI
34 Kim KY, Kim CN. Airborne microbiological characteristics in public buildings of Korea. Build Environ. 2007;42(5):2188-2196.
35 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.   DOI
36 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.   DOI