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

References

• 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.
   PubMed Web of Science ®Google Scholar
• Ríos J-L. Chemical constituents and pharmacological properties of Poria cocos. Planta Med. 2011;77(7):681–691.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Guan D, McCarthy SA, Wood J, et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898.
   Web of Science ®Google Scholar
• Krueger F, James F, Ewels P, et al. 2021. FelixKrueger/TrimGalore: v0.6.7-doi via Zenodo. Zenodo,
   Google Scholar
• Vaser R, Sović I, Nagarajan N, et al. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017;27(5):737–746.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinf. 2009;10(1):1–9.
   PubMedGoogle Scholar
• 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.
   Web of Science ®Google Scholar
• Min B, Grigoriev IV, Choi I-G. FunGAP: fungal genome annotation pipeline using evidence-based gene model evaluation. Bioinformatics. 2017;33(18):2936–2937.
   Web of Science ®Google Scholar
• Jones P, Binns D, Chang H-Y, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236–1240.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLOS One. 2010;5(3):e9490.
   PubMed Web of Science ®Google Scholar
• Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):1–14.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar