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Draft Genome Sequence of the Reference Strain of the Korean Medicinal Mushroom Wolfiporia cocos KMCC03342

  • Bogun Kim (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Byoungnam Min (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Jae-Gu Han (Mushroom Research Division, National Institute of Horticultural and Herbal Science, RDA) ;
  • Hongjae Park (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Seungwoo Baek (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Subin Jeong (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • In-Geol Choi (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
  • 투고 : 2022.02.17
  • 심사 : 2022.08.01
  • 발행 : 2022.08.31

초록

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.

키워드

과제정보

This study was funded by the Cooperative Research Program for the National Agricultural Genome Program, Rural Development Administration, Republic of Korea (project no. PJ01337602) and a National Research Foundation of Korea (NRF) grant funded by the government of the Republic of Korea (MEST) (grant NRF-2019R1A2C1089704). The authors were supported by Korea University grant.

참고문헌

  1. Yang L, Tang J, Chen J-J, et al. Transcriptome analysis of three cultivars of Poria cocos reveals genes related to the biosynthesis of polysaccharides. J Asian Nat Prod Res. 2019;21(5):462-475. https://doi.org/10.1080/10286020.2018.1494159
  2. Rios J-L. Chemical constituents and pharmacological properties of Poria cocos. Planta Med. 2011; 77(7):681-691. https://doi.org/10.1055/s-0030-1270823
  3. Shu S, Chen B, Zhou M, et al. De novo sequencing and transcriptome analysis of Wolfiporia cocos to reveal genes related to biosynthesis of triterpenoids. PLOS One. 2013;8(8):e71350.
  4. Cheng S, Swanson K, Eliaz I, et al. Pachymic acid inhibits growth and induces apoptosis of pancreatic cancer in vitro and in vivo by targeting ER stress. PLoS One. 2015;10(4):e0122270.
  5. Floudas D, Binder M, Riley R, et al. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012; 336(6089):1715-1719. https://doi.org/10.1126/science.1221748
  6. Cao S, Yang Y, Bi G, et al. Genomic and transcriptomic insight of giant sclerotium formation of wood-decay fungi. Front Microbiol. 2021;12:746121.
  7. Luo H, Qian J, Xu Z, et al. The Wolfiporia cocos genome and transcriptome shed light on the formation of its edible and medicinal sclerotium. Genomics Proteomics Bioinformatics. 2020;18(4):455-467. https://doi.org/10.1016/j.gpb.2019.01.007
  8. Min B, Yoon H, Park J, et al. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements. PLOS ONE. 2020;15(1):e0227923.
  9. Chin C-S, Peluso P, Sedlazeck FJ, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016;13(12):1050-1054. https://doi.org/10.1038/nmeth.4035
  10. Koren S, Walenz BP, Berlin K, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722-736. https://doi.org/10.1101/gr.215087.116
  11. Guan D, McCarthy SA, Wood J, et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896-2898. https://doi.org/10.1093/bioinformatics/btaa025
  12. Krueger F, James F, Ewels P, et al. 2021. FelixKrueger/TrimGalore: v0.6.7-doi via Zenodo. Zenodo,
  13. Vaser R, Sovi c I, Nagarajan N, et al. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017;27(5):737-746. https://doi.org/10.1101/gr.214270.116
  14. 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.
  15. Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinf. 2009;10(1):1-9.
  16. Manni M, Berkeley MR, Seppey M, et al. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647-4654. https://doi.org/10.1093/molbev/msab199
  17. Min B, Grigoriev IV, Choi I-G. FunGAP: fungal genome annotation pipeline using evidence-based gene model evaluation. Bioinformatics. 2017;33(18):2936-2937. https://doi.org/10.1093/bioinformatics/btx353
  18. Jones P, Binns D, Chang H-Y, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236-1240. https://doi.org/10.1093/bioinformatics/btu031
  19. Blin K, Shaw S, Kloosterman AM, et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 2021;49(W1):W29-W35. https://doi.org/10.1093/nar/gkab335
  20. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLOS One. 2010;5(3):e9490.
  21. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):1-14. https://doi.org/10.1186/s13059-018-1612-0
  22. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-780. https://doi.org/10.1093/molbev/mst010
  23. Steenwyk JL, Buida TJ III, Li Y, et al. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biol. 2020;18(12):e3001007.