Acknowledgement
This work was supported by a grant from the National Natural Science Foundation of China (31860177), General Project of Basic Research Program in Yunnan Province (202101AT070218), the Reserve Talents for Young and Middle-aged Academic and Technical Leaders of the Yunnan Province (202205AC160044).
References
- Erken MT, Cansaran-Duman D, Tanman U. In silico prediction of type I PKS gene modules in nine lichenized fungi. Biotechnol Biotec Eq. 2021;35(1):376-383. https://doi.org/10.1080/13102818.2021.1879679
- Elkhateeb WA, Ghwas DEE, Daba GM. Lichens uses surprising uses of lichens that improve human life. J Biomed Res Environ Sci. 2022;3(2):189-194. https://doi.org/10.37871/jbres1420
- Calcott MJ, Ackerley DF, Knight A, et al. Secondary metabolism in the lichen symbiosis. Chem Soc Rev. 2018;47(5):1730-1760. https://doi.org/10.1039/C7CS00431A
- Kim W, Liu R, Woo S, et al. Linking a gene cluster to atranorin, a major cortical substance of lichens, through genetic dereplication and heterologous expression. mBio. 2021;12(3):e01111-21. https://doi.org/10.1128/mBio.01111-21
- Devashree PA, Dikshit A. Lichens: fungal symbionts and their secondary metabolites. In: Joginder S and Praveen G, editors. New and future developments in microbial biotechnology and bioengineering. Amsterdam: Elsevier Science B.V; 2021. p. 107-115.
- Cornejo A, Salgado F, Caballero J, et al. Secondary metabolites in Ramalina terebrata detected by UHPLC/ESI/MS/MS and identification of parietin as tau protein inhibitor. Int J Mol Sci. 2016;17(8):1303.
- Abdel-Hameed M, Bertrand RL, Piercey-Normore MD, et al. Putative identification of the usnic acid biosynthetic gene cluster by de novo whole-genome sequencing of a lichen-forming fungus. Fungal Biol. 2016;120(3):306-316. https://doi.org/10.1016/j.funbio.2015.10.009
- Nybakken L, Solhaug KA, Bilger W, et al. The lichens Xanthoria elegans and Cetraria islandica maintain a high protection against UV-B radiation in arctic habitats. Oecologia. 2004;140(2):211-216. https://doi.org/10.1007/s00442-004-1583-6
- Wang HY, Li HM, Shi N, et al. The HPLC analysis of the lichen substances in five species of Xanthoria (Ascomycota). Mycosystema. 2003;22(4):536-541.
- Mamut R, Abbas A. The determination of usnic acid by HPLC method in Xanthoria elegans and their antibacterial activity. Food Sci Technol. 2012;37(8):216-219.
- Basile A, Rigano D, Loppi S, et al. Antiproliferative, antibacterial and antifungal activity of the lichen Xanthoria parietina and its secondary metabolite parietin. Int J Mol Sci. 2015;16(4):7861-7875. https://doi.org/10.3390/ijms16047861
- Gausla Y, Ustvedt EM. Is parietin a UV-B or a blue-light screening pigment in the lichen Xanthoria parietina? Photochem Photobiol Sci. 2003;2(4):424-432. https://doi.org/10.1039/b212532c
- Gagunashvili AN, Davidsson SP, Jonsson ZO, et al. Cloning and heterologous transcription of a polyketide synthase gene from the lichen Solorina crocea. Mycol Res. 2009;113(3):354-363. https://doi.org/10.1016/j.mycres.2008.11.011
- Armaleo D, Sun X, Culberson C. Insights from the first putative biosynthetic gene cluster for a lichen depside and depsidone. Mycologia. 2011;103(4):741-754. https://doi.org/10.3852/10-335
- Sabatini M, Comba S, Altabe S, et al. Biochemical characterization of the minimal domains of an iterative eukaryotic polyketide synthase. Febs J. 2018;285(23):4494-4511. https://doi.org/10.1111/febs.14675
- Cox RJ. Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem. 2007;5(13):2010-2026. https://doi.org/10.1039/b704420h
- Kage H, Riva E, Parascandolo JS, et al. Chemical chain termination resolves the timing of ketoreduction in a partially reducing iterative type I polyketide synthase. Org Biomol Chem. 2015;13(47):11414-11417. https://doi.org/10.1039/C5OB02009C
- Grau MF, Entwistle R, Chiang YM, et al. Hybrid transcription factor engineering activates the silent secondary metabolite gene cluster for (+)-asperlin in Aspergillus nidulans. ACS Chem Biol. 2018;13(11):3193-3205. https://doi.org/10.1021/acschembio.8b00679
- Park SY, Choi J, Lee GW, et al. Draft genome sequence of Umbilicaria muehlenbergii KoLRILF000956, a lichen-forming fungus amenable to genetic manipulation. Genome Announc. 2014;2(2):e00357-14.
- Yamamoto Y, Mizuguchi R, Yamada Y. Tissue cultures of Usnea rubescens and Ramalina yasudae and production of usnic acid in their cultures. Agric Biol Chem. 1985;49(11):3347-3348. https://doi.org/10.1271/bbb1961.49.3347
- Luo R, Liu B, Xie Y, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2015;4(1):1-16. https://doi.org/10.1186/s13742-015-0069-2
- Bao W, Kojima K, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6(1):11.
- Kapitonov V, 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
- Lowe T, Eddy S. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955-964. https://doi.org/10.1093/nar/25.5.955
- Lagesen K, Hallin P, Rodland E, et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-3108. https://doi.org/10.1093/nar/gkm160
- Kalvari I, Nawrocki E, Argasinska J, et al. Noncoding RNA analysis using the rfam database. Curr Protoc Bioinformatics. 2018;62(1):e51.
- Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005;33(2):465-467. https://doi.org/10.1093/nar/gki458
- Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004;20(16):2878-2879. https://doi.org/10.1093/bioinformatics/bth315
- Korf I. Gene finding in novel genomes. BMC Bioinf. 2004;5(1):1-9. https://doi.org/10.1186/1471-2105-5-59
- Haas BJ, Salzberg SL, Zhu W, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008;9(1):R7-22. https://doi.org/10.1186/gb-2008-9-1-r7
- Zhang D, Yu J, Ma C, et al. Genomic analysis of the mycoparasite Pestalotiopsis sp. PG52. Pol J Microbiol. 2021;70(2):189-199. https://doi.org/10.33073/pjm-2021-016
- 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
- Ahuja M, Chiang YM, Chang SL, et al. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc. 2012;134(19):8212-8221. https://doi.org/10.1021/ja3016395
- Araki Y, Awakawa T, Matsuzaki M, et al. Complete biosynthetic pathways of ascofuranone and ascochlorin in Acremonium egyptiacum. Proc Natl Acad Sci U S A. 2019;116(17):8269-8274. https://doi.org/10.1073/pnas.1819254116
- Kaneko A, Morishita Y, Tsukada K, et al. Postgenomic approach based discovery of alkylresorcinols from a cricket-associated fungus, Penicillium soppi. Org Biomol Chem. 2019;17(21):5239-5243. https://doi.org/10.1039/C9OB00807A
- Zabala AO, Chooi YH, Choi MS, et al. Fungal polyketide synthase product chain-length control by partnering thiohydrolase. ACS Chem Biol. 2014;9(7):1576-1586. https://doi.org/10.1021/cb500284t
- Nguyen HT, Ketha A, Kukavica B, et al. Anti-inflammatory potential of lichens and its substances. In: Vinay Bharadwaj T, editor. Inflammatory bowel disease. Reno (NV): MedDocs Publishers; 2021. p. 1-9.
- Wang Y, Geng C, Yuan X, et al. Identification of a putative polyketide synthase gene involved in usnic acid biosynthesis in the lichen Nephromopsis pallescens. PLoS One. 2018;13(7):e0199110.
- Kroken S, Glass NL, Taylor JW, et al. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc Natl Acad Sci U S A. 2003;100(26):15670-15675. https://doi.org/10.1073/pnas.2532165100
- Lim FY, Hou Y, Chen Y, et al. Genome-based cluster deletion reveals an endocrocin biosynthetic pathway in Aspergillus fumigatus. Appl Environ Microbiol. 2012;78(12):4117-4125.
- Pizarro D, Divakar PK, Grewe F, et al. Genome-wide analysis of biosynthetic gene cluster reveals correlated gene loss with absence of usnic acid in lichen-forming fungi. Genome Biol Evol. 2020;12(10):1858-1868. https://doi.org/10.1093/gbe/evaa189
- Ugai T, Minami A, Fujii R, et al. Heterologous expression of highly reducing polyketide synthase involved in betaenone biosynthesis. Chem Commun. 2015;51(10):1878-1881. https://doi.org/10.1039/C4CC09512J
- Gerasimova JV, Beck A, Werth S, et al. High diversity of type I polyketide genes in Bacidia rubella as revealed by the comparative analysis of 23 lichen genomes. J Fungi. 2022;8(5):449.
- Punya J, Swangmaneecharern P, Pinsupa S, et al. Phylogeny of type I polyketide synthases (PKSs) in fungal entomopathogens and expression analysis of PKS genes in Beauveria bassiana BCC 2660. Fungal Biol. 2015;119(6):538-550. https://doi.org/10.1016/j.funbio.2015.02.005
- Gallo A, Ferrara M, Perrone G. Phylogenetic study of polyketide synthases and nonribosomal peptide synthetases involved in the biosynthesis of mycotoxins. Toxins. 2013;5(4):717-742. https://doi.org/10.3390/toxins5040717