{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:27:22Z","timestamp":1790681242742,"version":"4.1.0"},"reference-count":13,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T00:00:00Z","timestamp":1731801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CIMB"],"abstract":"<jats:p>Efficient RNA isolation from filamentous fungi is crucial for gene expression studies, but it poses significant technical challenges due to the robust cell walls and susceptibility of RNA to degradation by ribonucleases. This study presents the effectiveness of two RNA isolation protocols for four species of filamentous fungi: Penicillium crustosum, Penicillium rubens, Penicillium griseofulvum, and Aspergillus fumigatus. Both protocols utilized Fenzol Plus for cell lysis but varied in the mechanical disruption methods: bead-beating versus manual vortexing. The results show that the bead-beater method (Protocol 1) yielded significantly higher RNA quantities, with better purity and integrity, as demonstrated by higher A260\/A280 and A260\/A230 ratios. RNA concentrations ranged from 30 to 96 \u00b5g\/g of dry biomass in Penicillium species and up to 52 \u00b5g\/g in A. fumigatus. The use of chloroform in Protocol 1 also enhanced RNA purity, effectively separating contaminants such as DNA, proteins, and polysaccharides. This optimized protocol is highly efficient and can be applied in routine laboratories handling large numbers of fungal samples, making it a robust method for downstream applications such as cDNA synthesis and transcriptome analysis.<\/jats:p>","DOI":"10.3390\/cimb46110778","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T06:57:54Z","timestamp":1732172274000},"page":"13050-13057","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Optimized Protocol for RNA Isolation from Penicillium spp. and Aspergillus fumigatus Strains"],"prefix":"10.3390","volume":"46","author":[{"given":"Aleksandra","family":"Siniecka-Kotula","sequence":"first","affiliation":[{"name":"Faculty of Chemistry, Department of Biotechnology and Microbiology, Gdansk University of Technology, 80-233 Gda\u0144sk, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6476-7580","authenticated-orcid":false,"given":"Martyna","family":"Mroczy\u0144ska-Szel\u0105g","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, Department of Biotechnology and Microbiology, Gdansk University of Technology, 80-233 Gda\u0144sk, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7049-2536","authenticated-orcid":false,"given":"Anna","family":"Brillowska-D\u0105browska","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, Department of Biotechnology and Microbiology, Gdansk University of Technology, 80-233 Gda\u0144sk, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5421-6905","authenticated-orcid":false,"given":"Lucyna","family":"Holec-G\u0105sior","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, Department of Biotechnology and Microbiology, Gdansk University of Technology, 80-233 Gda\u0144sk, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5294","DOI":"10.1021\/bi00591a005","article-title":"Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease","volume":"18","author":"Chirgwin","year":"1979","journal-title":"Biochemistry"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1007\/s12010-008-8289-x","article-title":"An improved RNA isolation method for filamentou fungus Blakeslea trispora rich in polysaccharides","volume":"160","author":"Li","year":"2010","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zeng, Y., and Yang, T. (2002). RNA isolation from highly viscous samples rich in polyphenols and polysaccharides. Plant Mol. Biol. Rep., 20.","DOI":"10.1007\/BF02772130"},{"key":"ref_4","first-page":"1","article-title":"A simple and rapid method for RNA isolation from plant tissues with high phenolic compounds and polysaccharides","volume":"184","author":"Chan","year":"2007","journal-title":"Protoc. Exch."},{"key":"ref_5","first-page":"5","article-title":"A versatile fungal RNA extraction protocol for filamentous fungi","volume":"55","author":"Bluhm","year":"2008","journal-title":"Fungal Genet. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/0003-2697(87)90021-2","article-title":"Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction","volume":"162","author":"Chomczynski","year":"1987","journal-title":"Anal. Biochem."},{"key":"ref_7","first-page":"569","article-title":"Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.)","volume":"387","author":"Garg","year":"2009","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Jiang, H., Lei, R., Ding, S.W., and Zhu, S. (2014). Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-182"},{"key":"ref_9","first-page":"3","article-title":"Fungal genomics challenges the classical concept of secondary metabolism","volume":"17","author":"Lange","year":"2018","journal-title":"Mycol. Prog."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Cort\u00e9s-Maldonadoa, L., Marcial-Quinob, J., G\u00f3mez-Manzoc, S., Fierroa, F., and Tomasinia, A. (2020). A method for the extraction of high quality fungal RNA suitable for RNA-seq. J. Microbiol. Methods, 170.","DOI":"10.1016\/j.mimet.2020.105855"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.ejbt.2013.12.009","article-title":"Comparison of different methods for total RNA extraction from sclerotia of Rhizoctonia solani","volume":"17","author":"Shu","year":"2014","journal-title":"Electron. J. Biotechnol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.colsurfb.2006.03.006","article-title":"A simple and convenient approach for isolating RNA from highly viscous plant tissue rich in polysaccharides","volume":"49","author":"Li","year":"2006","journal-title":"Colloids Surf. B Biointerfaces"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.mimet.2012.01.011","article-title":"Comparison of different bead-beating RNA extraction strategies: An optimized method for filamentous fungi","volume":"88","author":"Leite","year":"2012","journal-title":"J. Microbiol. Methods"}],"container-title":["Current Issues in Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1467-3045\/46\/11\/778\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:33:49Z","timestamp":1760114029000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1467-3045\/46\/11\/778"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,17]]},"references-count":13,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["cimb46110778"],"URL":"https:\/\/doi.org\/10.3390\/cimb46110778","relation":{},"ISSN":["1467-3045"],"issn-type":[{"value":"1467-3045","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,17]]}}}