Sequence Validation for the Identification of the White-Rot Fungi Bjerkandera in Public Sequence Databases |
Jung, Paul Eunil
(School of Biological Sciences, Seoul National University)
Fong, Jonathan J. (School of Biological Sciences, Seoul National University) Park, Myung Soo (School of Biological Sciences, Seoul National University) Oh, Seung-Yoon (School of Biological Sciences, Seoul National University) Kim, Changmu (National Institute of Biological Resources, Environmental Research Complex) Lim, Young Woon (School of Biological Sciences, Seoul National University) |
1 | Nunez M, Ryvarden L. 2001. East Asian Polypores. Vol. II. Fungiflora, Oystese, Norway. |
2 | Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K-H, Koljalg U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 1: e59. DOI |
3 | Park MS, Fong JJ, Lee H, Oh S-Y, Jung PE, Min YJ, et al. 2013. Delimitation of Russula subgenus Amoenula in Korea using three molecular markers. Mycobiology 41: 191-201. DOI ScienceOn |
4 | Rogers S, Bendich A. 1994. Extraction of total cellular DNA from plants, algae and fungi, pp. 183-190. In Gelvin S, Schilperoort R (eds.). Plant Molecular Biology Manual. Springer, The Netherlands. |
5 | Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A. 2002. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res. 2: 495-517. DOI |
6 | Romero E, Speranza M, Garcia-Guinea J, Martinez AT, Martinez MJ. 2007. An anamorph of the white-rot fungus Bjerkandera adusta capable of colonizing and degrading compact disc components. FEMS Microbiol. Lett. 275: 122-129. DOI ScienceOn |
7 | Ryvarden L, Gilbertson RL. 1993. European Polypores. Part 1. Fungiflora, Oslo. |
8 | Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc. Natl. Acad. Sci. USA 109: 6241-6246. DOI ScienceOn |
9 | Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772-780. DOI ScienceOn |
10 | Lim YW, Lee JS, Jung HS. 2010. Fungal Flora of Korea. Basidiomycota: Hymenomycetes: Aphyllophorales, pp. 20-22. The National Institute of Biological Resources, Incheon, Korea. |
11 | Murrill WA. 1905. The Polyporaceae of North America - XIII. The described species of Bjerkandera, Trametes, and Coriolus. Bull. Torrey Bot. Club 32: 633-656. DOI ScienceOn |
12 | Choi YS, Seo JY, Lee H, Yoo J, Jung J, Kim JJ, Kim G-H. 2013. Decolorization and detoxification of wastewater containing industrial dyes by Bjerkandera adusta KUC9065. Water Air Soil Pollut. 225: 1-10. |
13 | Toda T, Hayakawa T, Mghalu J, Yaguchi S, Hyakumachi M. 2007. A new Rhizoctonia sp. closely related to Waitea circinata causes a new disease of creeping bentgrass. J. Gen. Plant Pathol. 73: 379-387. DOI ScienceOn |
14 | Tringe SG, Rubin EM. 2005. Metagenomics: DNA sequencing of environmental samples. Nat. Rev. Genet. 11: 805-814. DOI ScienceOn |
15 | Ueki H. 1936. Vegetations in the Kwa-San hill and the environs of Suigen. Bull. Agric. For. Coll. Suigen 5: 155. |
16 | Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172: 4238-4246. DOI |
17 | White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, pp. 315-322. In Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds.). PCR Protocols: A Guide to Methods and Applications. Academic Press, New York. |
18 | Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, et al. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719. DOI ScienceOn |
19 | Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. DOI ScienceOn |
20 | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. DOI ScienceOn |
21 | Frohlich-Nowoisky J, Pickersgill DA, Despres VR, Poschl U. 2009. High diversity of fungi in air particulate matter. Proc. Natl. Acad. Sci. USA 106: 12814-12819. DOI ScienceOn |
22 | Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol. 2: 113-118. DOI ScienceOn |
23 | Gilbertson RL, Ryvarden L. 1986. North American Polypores. Vol. I. Fungiflora, Oslo. |
24 | Ko KS, Jung HS, Ryvarden L. 2001. Phylogenetic relationships of Hapalopilus and related genera inferred from mitochondrial small subunit ribosomal DNA sequences. Mycologia 93: 270-276. DOI ScienceOn |
25 | Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. USA 101: 14812-14817. DOI ScienceOn |
26 | Jung HS. 1994. Floral studies on Korean wood-rotting fungi - on the flora of the Aphyllophorales (Basidiomycotina). Korean J. Mycol. 22: 62-99. 과학기술학회마을 |
27 | Bak WC, Lee B-H, Park Y-A, Kim H-S. 2011. Characteristics of bed-log of shiitake damaged by Bjerkandera adusta and antagonism between these two fungi. Korean J. Mycol. 39: 44-47. 과학기술학회마을 DOI ScienceOn |
28 | Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjokvist E, et al. 2013. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 105: 1350-1373. DOI ScienceOn |
29 | Bridge PD, Roberts PJ, Spooner BM, Panchal G. 2003. On the unreliability of published DNA sequences. New Phytol. 160: 43-48. DOI ScienceOn |
30 | Fell JW, Boekhout T, Fonseca A, Scorzetti G, Statzell-Tallman A. 2000. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int. J. Syst. Evol. Microbiol. 50: 1351-1371. DOI ScienceOn |
31 | Haritash AK, Kaushik CP. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J. Hazard. Mater. 169: 1-15. DOI ScienceOn |