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http://dx.doi.org/10.1080/12298093.2020.1756134

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)
Publication Information
Mycobiology / v.48, no.3, 2020 , pp. 240-244 More about this Journal
Abstract
Alternaria alternata JS-1623 is an endophytic fungus isolated from a stem tissue of Korean fir, Abies koreana. Ethyl acetate extracts of culture filtrates exhibited anti-inflammatory activity in LPS induced microglia BV-2 cell without cytotoxicity. Here we report a 33.67 Mb sized genome assembly of JS-1623 comprised of 13 scaffolds with N50 of 4.96 Mb, and 92.41% of BUSCO completeness. GC contents were 50.97%. Of the 11,197 genes annotated, gene families related to the biosynthesis of secondary metabolites or transcription factors were identified.
Keywords
Abies koreana; Alternaria alternata; endophytes; whole genome sequence;
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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