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) |
1 | 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. DOI |
2 | Min B, Grigoriev IV, Choi I-G. FunGAP: fungal genome annotation pipeline using evidence-based gene model evaluation. Bioinformatics. 2017;33(18):2936-2937. DOI |
3 | Jones P, Binns D, Chang H-Y, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236-1240. DOI |
4 | 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. DOI |
5 | Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLOS One. 2010;5(3):e9490. |
6 | Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):1-14. DOI |
7 | Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-780. DOI |
8 | 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. |
9 | 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. DOI |
10 | Rios J-L. Chemical constituents and pharmacological properties of Poria cocos. Planta Med. 2011; 77(7):681-691. DOI |
11 | 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. |
12 | 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. |
13 | 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. DOI |
14 | 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. |
15 | 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. DOI |
16 | 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. DOI |
17 | 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. |
18 | 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. DOI |
19 | Guan D, McCarthy SA, Wood J, et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896-2898. DOI |
20 | Krueger F, James F, Ewels P, et al. 2021. FelixKrueger/TrimGalore: v0.6.7-doi via Zenodo. Zenodo, |
21 | 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. DOI |
22 | 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. |
23 | Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinf. 2009;10(1):1-9. |
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