Mycobiology

The Korean Society of Mycology (한국균학회)
권호 표지
DOI QR코드

DOI QR Code

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)
  • Received : 2020.03.17
  • Accepted : 2020.04.08
  • Published : 2020.06.30
Download PDF
⟨ Previous Next ⟩

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

References

  1. Lee HB, Patriarca A, Magan N. Alternaria in food: ecophysiology, mycotoxin production and toxicology. Mycobiology. 2015;43(2):93-106. https://doi.org/10.5941/MYCO.2015.43.2.93
  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. https://doi.org/10.1080/12298093.2018.1454007
  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. https://doi.org/10.3920/WMJ2008.x013
  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. https://doi.org/10.1016/j.fitote.2014.09.017
  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. https://doi.org/10.3390/md16110402
  7. 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. https://doi.org/10.1016/j.bmc.2014.08.039
  8. 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. https://doi.org/10.1080/14786419.2013.771352
  9. 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. https://doi.org/10.1111/jam.14138
  10. 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. https://doi.org/10.1038/ja.2017.39
  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. https://doi.org/10.1093/molbev/msy096
  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. https://doi.org/10.1038/nmeth.1376
  15. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315-327. https://doi.org/10.1016/j.ygeno.2010.03.001
  16. Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res. 2010;20(9):1165-1173. https://doi.org/10.1101/gr.101360.109
  17. 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. https://doi.org/10.1093/bioinformatics/btt702
  18. Huang S, Chen Z, Huang G, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012;22(8):1581-1588. https://doi.org/10.1101/gr.133652.111
  19. Boetzer M, Henkel CV, Jansen HJ, et al. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27(4):578-579. https://doi.org/10.1093/bioinformatics/btq683
  20. Boetzer M, Pirovano W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics. 2014;15(1):211. https://doi.org/10.1186/1471-2105-15-211
  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. https://doi.org/10.1186/1471-2105-13-S14-S8
  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. https://doi.org/10.1093/molbev/msx319
  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. https://doi.org/10.1093/nar/gkh379
  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. https://doi.org/10.1093/nar/gkz310
  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. https://doi.org/10.1093/bioinformatics/btn058
  26. Park J, Lee S, Choi J, et al. Fungal cytochrome P450 database. BMC Genomics. 2008;9(1):402. https://doi.org/10.1186/1471-2164-9-402
  27. Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob Dna. 2015;6:11. https://doi.org/10.1186/s13100-015-0041-9
  28. 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. https://doi.org/10.1038/nrg2165-c1
  29. Smit AFA, Hubley R, Green P. RepeatMasker. [Internet]. 2015. Available from: http://repeatmasker.org.
  30. Chan PP, Lowe TM. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol. 2019;1962:1-14. https://doi.org/10.1007/978-1-4939-9173-0_1
  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. https://doi.org/10.1093/nar/gks1005