Draft Genome Sequence of Alternaria alternata JS-1623, a Fungal Endophyte of Abies koreana |
Park, Sook-Young
(Department of Plant Medicine, Sunchon National University)
Jeon, Jongbum (Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University) Kim, Jung A. (Microbiology Resources Division, National Institute of Biological Resources) Jeon, Mi Jin (Microbiology Resources Division, National Institute of Biological Resources) Jeong, Min-Hye (Department of Plant Medicine, Sunchon National University) Kim, Youngmin (Department of Plant Medicine, Sunchon National University) Lee, Yerim (Department of Plant Medicine, Sunchon National University) Chung, Hyunjung (Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University) Lee, Yong-Hwan (Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University) Kim, Soonok (Microbiology Resources Division, National Institute of Biological Resources) |
1 | Lee HB, Patriarca A, Magan N. Alternaria in food: ecophysiology, mycotoxin production and toxicology. Mycobiology. 2015;43(2):93-106. DOI |
2 | Luo H, Tao YQ, Fan XY, et al. Identification and characterization of Alternaria iridiaustralis causing leaf spot on iris ensata in China. Mycobiology. 2018;46(2):168-171. DOI |
3 | Ostry V. Alternaria mycotoxins: an overview of chemical characterization, producers, toxicity, analysis and occurrence in foodstuffs. World Mycotoxin J. 2008;1(2):175-188. DOI |
4 | Moharram AM, Zohri AA, Omar HM, et al. In vitro assessment of antimicrobial and anti-inflammatory potential of endophytic fungal metabolites extracts. Eur J Biol Res. 2017;7:234-244. |
5 | Wang XZ, Luo XH, Xiao J, et al. Pyrone derivatives from the endophytic fungus Alternaria tenuissima SP-07 of Chinese herbal medicine Salvia przewalskii. Fitoterapia. 2014;99:184-190. DOI |
6 | Shen L, Tian SJ, Song HL, et al. Cytotoxic tricycloalternarene compounds from endophyte Alternaria sp. W-1 associated with Laminaria japonica. Mar Drugs. 2018;16:pii: E402. DOI |
7 | Lee C, Kim S, Li W, et al. Bioactive secondary metabolites produced by an endophytic fungus Gaeumannomyces sp. JS0464 from a maritime haplophyte Phragmites communis. J Antibiot. 2017;70(6):737-742. DOI |
8 | Bashyal BP, Wellensiek BP, Ramakrishnan R, et al. Altertoxins with potent anti-HIV activity from Alternaria tenuissima QUE1Se, a fungal endophyte of Quercus emoryi. Bioorg Med Chem. 2014;22(21):6112-6116. DOI |
9 | Li DM, Zhang YH, Ji HX, et al. Tricycloalternarene derivatives from endophytic fungus Alternaria tenuissima SY-P-07. Nat Prod Res. 2013;27(20):1877-1881. DOI |
10 | Nguyen HT, Kim S, Yu NH, et al. Antimicrobial activities of an oxygenated cyclohexanone derivative isolated from Amphirosellinia nigrospora JS-1675 against various plant pathogenic bacteria and fungi. J Appl Microbiol. 2019;126(3):894-904. DOI |
11 | Simmons EG. Alternaria: an identification manual. Urecht (Netherlands): Centraalbureau voor Schimmelcultures; 2007. |
12 | Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547-1549. DOI |
13 | Jeon J, Park SY, Kim JA, et al. Draft genome sequence of Amphirosellinia nigrospora JS-1675, an endophytic fungus from Pteris cretica. Microbiol Resour Announc. 2019;8(20):pii:e00069-19. |
14 | Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods. 2009;6(S11):S6-S12. DOI |
15 | Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315-327. DOI |
16 | Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res. 2010;20(9):1165-1173. DOI |
17 | Boetzer M, Pirovano W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics. 2014;15(1):211. DOI |
18 | Leggett RM, Clavijo BJ, Clissold L, et al. NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. Bioinformatics. 2014;30(4):566-568. DOI |
19 | Huang S, Chen Z, Huang G, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012;22(8):1581-1588. DOI |
20 | Boetzer M, Henkel CV, Jansen HJ, et al. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27(4):578-579. DOI |
21 | Nadalin F, Vezzi F, Policriti A. GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics. 2012;13(S14):S8. DOI |
22 | Waterhouse RM, Seppey M, Simao FA, et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2018;35(3):543-548. DOI |
23 | Stanke M, Steinkamp R, Waack S, et al. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004;32(Web Server):W309-W312. DOI |
24 | Blin K, Shaw S, Steinke K, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47(W1):W81-W87. DOI |
25 | Park J, Park J, Jang S, et al. FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics. 2008;24(7):1024-1025. DOI |
26 | Park J, Lee S, Choi J, et al. Fungal cytochrome P450 database. BMC Genomics. 2008;9(1):402. DOI |
27 | Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob Dna. 2015;6:11. DOI |
28 | Chan PP, Lowe TM. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol. 2019;1962:1-14. DOI |
29 | Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008;9(5):411-412. Author reply 414. DOI |
30 | Smit AFA, Hubley R, Green P. RepeatMasker. [Internet]. 2015. Available from: http://repeatmasker.org. |
31 | Burge SW, Daub J, Eberhardt R, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013;41(D1):D226-D232. DOI |
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