DOI QR코드

DOI QR Code

Draft Genome Sequence of Xylaria grammica EL000614, a Strain Producing Grammicin, a Potent Nematicidal Compound

  • 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 (Animal Resources Division, National Institute of Biological Resources) ;
  • Jeon, Mi Jin (Microorganism Resources Division, National Institute of Biological Resources) ;
  • Yu, Nan Hee (Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Kim, Seulbi (Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Park, Ae Ran (Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Kim, Jin-Cheol (Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Lee, Yerim (Department of Plant Medicine, Sunchon National University) ;
  • Kim, Youngmin (Department of Plant Medicine, Sunchon National University) ;
  • Choi, Eu Ddeum (Department of Plant Medicine, Sunchon National University) ;
  • Jeong, Min-Hye (Department of Plant Medicine, Sunchon 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 (Microorganism Resources Division, National Institute of Biological Resources)
  • Received : 2021.02.01
  • Accepted : 2021.04.05
  • Published : 2021.06.30

Abstract

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.

Keywords

Acknowledgement

This work was supported by the National Institute of Biological Resources, funded by the Ministry of Environment of the Republic of Korea (projects NIBR201921101 and NIBR202021101).

References

  1. Kellogg J, Raja HA. Endolichenic fungi: a new source of rich bioactive secondary metabolites on the horizon. Phytochem Rev. 2017;16(2):271-293. https://doi.org/10.1007/s11101-016-9473-1
  2. Kim TY, Jang JY, Yu NH, et al. Nematicidal activity of grammicin produced by Xylaria grammica KCTC 13121BP against Meloidogyne incognita. Pest Manag Sci. 2018;74(2):384-391. https://doi.org/10.1002/ps.4717
  3. Edwards RL, Maitland DJ, Pittayakhajonwut P, et al. Metabolites of the higher fungi. Part 33. Grammicin, a novel bicyclic C7H6O4 furanopyranol from the fungus Xylaria grammica (Mont.) Fr. Perkin Trans. 2001;1(11):1296-1299.
  4. Wang A, Wang Z, Li Z, et al. BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach. Bioinformatics. 2018;34(12):2019-2028. https://doi.org/10.1093/bioinformatics/bty020
  5. Koren S, Walenz BP, Berlin K, et al. Canu: scalable and accurate long-read assembly via adaptive kmer weighting and repeat separation. Genome Res. 2017;27(5):722-736. https://doi.org/10.1101/gr.215087.116
  6. Walker BJ, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9(11):e112963. https://doi.org/10.1371/journal.pone.0112963
  7. 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
  8. Bruna T, Hoff KJ, Lomsadze A, et al. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP + and AUGUSTUS supported by a protein database. NAR Genom Bioinform. 2021;3:108.
  9. 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
  10. Artigot MP, Loiseau N, Laffitte J, et al. Molecular cloning and functional characterization of two CYP619 cytochrome P450s involved in biosynthesis of patulin in Aspergillus clavatus. Microbiology. 2009;155(Pt 5):1738-1747. https://doi.org/10.1099/mic.0.024836-0
  11. 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
  12. Park J, Lee S, Choi J, et al. Fungal cytochrome P450 database. BMC Genomics. 2008;9:402. https://doi.org/10.1186/1471-2164-9-402
  13. 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
  14. Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008;9(5):411-412. https://doi.org/10.1038/nrg2165-c1
  15. Smit AFA, Hubley R, Green P. RepeatMasker. 2015. Available from: http://repeatmasker.org.
  16. 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
  17. Burge SW, Daub J, Eberhardt R, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013;41(Database issue):D226-D232. https://doi.org/10.1093/nar/gks1005