IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

. 2023 Oct 06 ; 14 (1) : 21. [epub] 20231006

Status PubMed-not-MEDLINE Jazyk angličtina Země Bulharsko Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37803441
Odkazy

PubMed 37803441
PubMed Central PMC10559472
DOI 10.1186/s43008-023-00121-w
PII: 10.1186/s43008-023-00121-w
Knihovny.cz E-zdroje

Zobrazit více v PubMed

Alapont C, López-Mendoza MC, Gil JV, Martínez-Culebras PV. Mycobiota and toxigenic Penicillium species on two Spanish dry-cured ham manufacturing plants. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2014;31:93–104. doi: 10.1080/19440049.2013.849007. PubMed DOI

Alapont C, Martínez-Culebras PV, López-Mendoza MC. Determination of lipolytic and proteolytic activities of mycoflora isolated from dry-cured teruel ham. J Food Sci Technol. 2015;52:5250–5256. doi: 10.1007/s13197-014-1582-5. PubMed DOI PMC

Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 1997;25:4692–4693. doi: 10.1093/nar/25.22.4692. PubMed DOI PMC

Amoa-Awua WK, Frisvad JC, Sefa-Dedeh S, Jakobsen M. The contribution of moulds and yeasts to the fermentation of 'agbelima' cassava dough. J Appl Microbiol. 1997;83:288–296. doi: 10.1046/j.1365-2672.1997.00227.x. PubMed DOI

Andjic V, Pegg GS, Carnegie AJ, Callister A, Hardy GE, Burgess TI. Teratosphaeria pseudoeucalypti, new cryptic species responsible for leaf blight of eucalyptus in subtropical and tropical Australia. Plant Pathol. 2010;59:900–912. doi: 10.1111/j.1365-3059.2010.02308.x. DOI

Andjic V, Carnegie AJ, Pegg GS, Hardy GESJ, Maxwell A, Crous PW, Pérez C, Wingfield MJ, Burgess TI. 23 years of research on Teratosphaeria leaf blight of Eucalyptus. For Ecol Manag. 2019;443:19–27. doi: 10.1016/j.foreco.2019.04.013. DOI

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data [Online]. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. In.: Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom

Anelli P, Peterson SW, Haidukowski M, Logrieco AF, Moretti A, et al. Penicillium gravinicasei, a new species isolated from cave cheese in Apulia, Italy. Int J Food Microbiol. 2018;282:66–70. doi: 10.1016/j.ijfoodmicro.2018.06.006. PubMed DOI

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25:25–29. doi: 10.1038/75556. PubMed DOI PMC

Avery SV, Singleton I, Magan N, Goldman GH. The fungal threat to global food security. Fungal Biol. 2019;123:555–557. doi: 10.1016/j.funbio.2019.03.006. PubMed DOI

Aylward J, Roets F, Dreyer LL, Wingfield MJ. Teratosphaeria stem canker of eucalyptus: two pathogens, one devastating disease. Mol Plant Pathol. 2019;20:8–19. doi: 10.1111/mpp.12758. PubMed DOI PMC

Aylward J, Havenga M, Dreyer LL, Roets F, Wingfield BD, Pérez CA, Ramírez-Berrutti N, Carnegie AJ, Wingfield MJ. Genetic diversity of Teratosphaeria pseudoeucalypti in Eucalyptus plantations in Australia and Uruguay. Australas Plant Pathol. 2021;50:639–649. doi: 10.1007/s13313-021-00800-5. DOI

Aylward J, Wingfield MJ, Roets F, Wingfield BD. A high-quality fungal genome assembly resolved from a sample accidentally contaminated by multiple taxa. Biotechniques. 2022;72:39–50. doi: 10.2144/btn-2021-0097. PubMed DOI

Baka AM, Papavergou EJ, Pragalaki T, Bloukas JG, Kotzekidou P. Effect of selected autochthonous starter cultures on processing and quality characteristics of Greek fermented sausages. LWT Food Sci Technol. 2011;44:54–61. doi: 10.1016/j.lwt.2010.05.019. DOI

Balocchi F, Wingfield MJ, Ahumada R, Barnes I. Pewenomyces kutranfy gen nov. et sp. nov. causal agent of an important canker disease on Araucaria araucana in Chile. Plant Pathol. 2021;70:1243–1259. doi: 10.1111/ppa.13353. DOI

Balocchi F, Marincowitz S, Wingfield MJ, Ahumada R, Barnes I. Three new species of Pewenomyces (Coryneliaceae) from Araucaria araucana in Chile. Mycol Prog. 2022;21:1–23. doi: 10.1007/s11557-022-01840-x. PubMed DOI

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–477. doi: 10.1089/cmb.2012.0021. PubMed DOI PMC

Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11. doi: 10.1186/s13100-015-0041-9. PubMed DOI PMC

Benny GL, Samuelson DA, Kimbrough JW. Studies on the Coryneliales. I. Fitzpatrickella, a monotypic genus on the fruits of Drimys. Bot Gaz. 1985;146:232–237. doi: 10.1086/337519. DOI

Benny GL, Samuelson DA, Kimbrough JW. Studies on the Coryneliales. IV. Caliciopsis, Coryneliopsis, and Coryneliospora. Bot Gaz. 1985;146:437–448. doi: 10.1086/337544. DOI

Berbegal M, Ramón-Albalat A, León M, Armengol J. Evaluation of long-term protection from nursery to vineyard provided by Trichoderma atroviride SC1 against fungal grapevine trunk pathogens. Pest Manag Sci. 2020;76:967–977. doi: 10.1002/ps.5605. PubMed DOI

Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 2021;49:W29–W35. doi: 10.1093/nar/gkab335. PubMed DOI PMC

Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML et al (2012) Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol.154:87–97. Erratum in: Int J Food Microbiol 156:301 PubMed

Burgess TI, Wingfield MJ. Pathogens on the move: a 100-year global experiment with planted eucalypts. Bioscience. 2017;67:14–25. doi: 10.1093/biosci/biw146. DOI

Bushnell B (2020) BBTools software package. http://sourceforge.net/projects/bbmap

Butin H. Two new Caliciopsis spp. on Chilean conifers. Phytopathol Z. 1970;69:71–77. doi: 10.1111/j.1439-0434.1970.tb03903.x. DOI

Calvo AM, Wilson RA, Bok JW, Keller NP. Relationship between secondary metabolism and fungal development. Microbiol Mol Biol Rev. 2002;66:447–459. doi: 10.1128/MMBR.66.3.447-459.2002. PubMed DOI PMC

Cândido TDS, Da Silva AC, Guimarães LMDS, Ferraz HGM, Borges Júnior N, et al. Teratosphaeria pseudoeucalypti on eucalyptus in Brazil. Trop Plant Pathol. 2014;39:407–412. doi: 10.1590/S1982-56762014000500008. DOI

Challis R, Richards E, Rajan J, Cochrane G, Blaxter M. BlobToolKit interactive quality assessment of genome assemblies. G3 Genes|genom|genet. 2020;10:1361–1374. doi: 10.1534/g3.119.400908. PubMed DOI PMC

Chernomor O, von Haeseler A, Minh BQ. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 2016;65:997–1008. doi: 10.1093/sysbio/syw037. PubMed DOI PMC

Chet I, Harman GE, Baker R. Trichoderma hamatum: Its hyphal interactions with Rhizoctonia solani and Pythium spp. Microb Ecol. 1981;7:29–38. doi: 10.1007/BF02010476. PubMed DOI

Crous PW, Boers J, Holdom D, Osieck STV, et al. Fungal planet description sheets: 1383–1435. Persoonia Mol Phylogeny Evol Fungi. 2022;48:261–371. doi: 10.3767/persoonia.2022.48.08. PubMed DOI PMC

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol Biol Evol. 2020;37:291–294. doi: 10.1093/molbev/msz189. PubMed DOI PMC

Davies CR, Wohlgemuth F, Young T, Violet J, Dickinson M, et al. Evolving challenges and strategies for fungal control in the food supply chain. Fungal Biol Rev. 2021;36:15–26. doi: 10.1016/j.fbr.2021.01.003. PubMed DOI PMC

Duong TA, De Beer ZW, Wingfield BD, Wingfield MJ. Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum. Fungal Biol. 2013;117:411–421. doi: 10.1016/j.funbio.2013.04.005. PubMed DOI

Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461. doi: 10.1093/bioinformatics/btq461. PubMed DOI

EFSA Biohaz Panel (EFSA Panel on Biological Hazards) Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bover-Cid S, Chemaly M, et al. Scientific opinion on the microbiological safety of aged meat. EFSA J. 2023;21:e7745. PubMed PMC

Eichmeier A, Baránek M, Pidra M. Analysis of genetic diversity and phylogeny of partial coat protein domain in Czech and Italian GFLV isolates. Plant Prot Sci. 2010;46(4):145–148. doi: 10.17221/10/2010-PPS. DOI

Fabian SJ, Maust MD, Panaccione DG. Ergot alkaloid synthesis capacity of Penicillium camemberti. Appl Environ Microbiol. 2018;84:e01583–e1618. doi: 10.1128/AEM.01583-18. PubMed DOI PMC

Ferrocino I, Bellio A, Giordano M, Macori G, Romano A, et al. Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages. Appl Environ Microbiol. 2018;84:1–14. doi: 10.1128/AEM.02120-17. PubMed DOI PMC

Fitzpatrick HM. Monograph of the coryneliaceae. Mycologia. 1920;12:206–237. doi: 10.1080/00275514.1920.12016837. DOI

Fitzpatrick HM. Revisionary studies in the coryneliaceae. II. The genus caliciopsis. Mycologia. 1942;34:489–514. doi: 10.1080/00275514.1942.12020918. DOI

Flynn JM, Hubley R, Goubert C, Rosen J, Clark,, et al. RepeatModeler2 for automated genomic discovery of transposable element families. PNAS. 2020;117:9451–9457. doi: 10.1073/pnas.1921046117. PubMed DOI PMC

Frisvad JC. Penicillium / Penicillia in food production. In: Batt CA, Tortorello ML, editors. Encyclopedia of food microbiology. Elsevier; 2014. pp. 14–18.

Frisvad JC, Samson RA. Polyphasic taxonomy of Penicillium subgenus Penicillium. A guide to identification of food and air-borne terverticillate Penicillia and their mycotoxins. Stud Mycol. 2004;49:1–174.

Frisvad JC, Smedsgaard J, Larsen TO, Samson RA. Mycotoxins, drugs and other extrolites produced by species in Penicillium subgenus Penicillium. Stud Mycol. 2004;49:201–241.

Garnier L, Valence F, Pawtowski A, Auhustsinava-Galerne L, Frotté N, et al. Diversity of spoilage fungi associated with various French dairy products. Int J Food Microbiol. 2017;241:191–197. doi: 10.1016/j.ijfoodmicro.2016.10.026. PubMed DOI

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–652. doi: 10.1038/nbt.1883. PubMed DOI PMC

Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42:D699–D704. doi: 10.1093/nar/gkt1183. PubMed DOI PMC

Gupta VG, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, et al., editors. Biotechnology and biology of Trichoderma. Australia: Newnes; 2014.

Hale AR, Ruegger PM, Rolshausen P, Borneman J, Yang JI. Fungi associated with the potato taste defect in coffee beans from Rwanda. Bot Stud. 2022;63:17. doi: 10.1186/s40529-022-00346-9. PubMed DOI PMC

Haridas S, Albert R, Binder M, Bloem J, Labutti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, et al. 101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens. Stud Mycol. 2020;96:141–153. doi: 10.1016/j.simyco.2020.01.003. PubMed DOI PMC

Havenga M, Wingfield BD, Wingfield MJ, Dreyer LL, Roets F, Aylward J. Diagnostic markers for Teratosphaeria destructans and closely related species. Forest Pathol. 2020;50:e12645. doi: 10.1111/efp.12645. DOI

Hermosa R, Viterbo A, Chet I, Monte E. Plant-beneficial effects of Trichoderma and of its genes. Microbiology. 2012;158(1):17–25. doi: 10.1099/mic.0.052274-0. PubMed DOI

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–522. doi: 10.1093/molbev/msx281. PubMed DOI PMC

Hood IA, Chapman SJ, Gardner JF, Molony K. Seasonal development of septoria leaf blight in young Eucalyptus nitens plantations in New Zealand. Aust for. 2002;65:153–164. doi: 10.1080/00049158.2002.10674868. DOI

Horta MA, Filho JA, Murad NF, de Oliveira Santos E, Dos Santos CA, Mendes JS, Brandão MM, Azzoni SF, de Souza AP (2018) Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species. Sci Rep 8(1):1341 PubMed PMC

Houbraken J, Frisvad JC, Seifert KA, et al. New penicillin-producing Penicillium species and an overview of section Chrysogena. Persoonia. 2012;29:78–100. doi: 10.3767/003158512X660571. PubMed DOI PMC

Houbraken J, Visagie CM, Meijer M, Frisvad JC, Busby PE, et al. A taxonomic and phylogenetic revision of Penicillium section Aspergilloides. Stud Mycol. 2014;78:373–451. doi: 10.1016/j.simyco.2014.09.002. PubMed DOI PMC

Houbraken J, Wang L, Lee HB, Frisvad JC. New sections in Penicillium containing novel species producing patulin, pyripyropens or other bioactive compounds. Persoonia. 2016;36:299–314. doi: 10.3767/003158516X692040. PubMed DOI PMC

Houbraken J, Kocsubé S, Visagie CM, Yilmaz N, Wang XC, et al. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): an overview of families, genera, subgenera, sections, series and species. Stud Mycol. 2020;95:5–169. doi: 10.1016/j.simyco.2020.05.002. PubMed DOI PMC

Houbraken J, Visagie CM, Frisvad JC. Recommendations to prevent taxonomic misidentification of genome-sequenced fungal strains. Microbiol Resour Announc. 2021;10:e0107420. doi: 10.1128/MRA.01074-20. PubMed DOI PMC

Howell CR. Cotton seedling preemergence damping-off incited by Rhizopus oryzae and Pythium spp. and its biological control with Trichoderma spp. Phytopathology. 2002;92(2):177–180. doi: 10.1094/PHYTO.2002.92.2.177. PubMed DOI

Hunter GC, Crous PW, Carnegie AJ, Burgess TI, Wingfield MJ. Mycosphaerella and Teratosphaeria diseases of Eucalyptus; easily confused and with serious consequences. Fungal Divers. 2011;50:145. doi: 10.1007/s13225-011-0131-z. DOI

Hyde KD, Tennakoon DS, Jeewon R, Bhat DJ, Maharachchikumbura SSN, et al. Fungal diversity notes 1036–1150: taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Divers. 2019;96:1–242. doi: 10.1007/s13225-019-00429-2. DOI

Hymery N, Vasseur V, Coton M, Mounier J, Jany JL, et al. Filamentous fungi and mycotoxins in cheese: a review. Compr Rev Food Sci Food Saf. 2014;13:437–456. doi: 10.1111/1541-4337.12069. PubMed DOI

Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21:241. doi: 10.1186/s13059-020-02154-5. PubMed DOI PMC

Jung YJ, Chung SH, Lee HK, Chun HS, Hong SB. Isolation and identification of fungi from a meju contaminated with aflatoxins. J Microbiol Biotechnol. 2012;22:1740–1748. doi: 10.4014/jmb.1207.07048. PubMed DOI

Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–467. doi: 10.1159/000084979. PubMed DOI

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34:D354–D357. doi: 10.1093/nar/gkj102. PubMed DOI PMC

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2017;20:1160–1166. doi: 10.1093/bib/bbx108. PubMed DOI PMC

Kaur P, Dua K. (2022) Recent trends in fungal dairy fermented foods. Adv Dairy Microb Prod, pp 41–57

Keller O, Kollmar M, Stanke M, Waack S. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics. 2011;27:757–763. doi: 10.1093/bioinformatics/btr010. PubMed DOI

Kemler M, Garnas J, Wingfield MJ, Gryzenhout M, Pillay K-A, Slippers B. Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity. PLoS ONE. 2013;8:e81718. doi: 10.1371/journal.pone.0081718. PubMed DOI PMC

Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, et al. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 2010;47:736–741. doi: 10.1016/j.fgb.2010.06.003. PubMed DOI PMC

Kim DH, Kim SH, Kwon SW, Lee JK, Hong SB. The mycobiota of air inside and outside the Meju fermentation room and the origin of Meju Fungi. Mycobiology. 2015;43:258–265. doi: 10.5941/MYCO.2015.43.3.258. PubMed DOI PMC

Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 2004;5:R7. doi: 10.1186/gb-2004-5-2-r7. PubMed DOI PMC

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453–4455. doi: 10.1093/bioinformatics/btz305. PubMed DOI PMC

Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, et al. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 2011;12:R40. doi: 10.1186/gb-2011-12-4-r40. PubMed DOI PMC

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Lazazzara V, Vicelli B, Bueschl C, Parich A, Pertot I, et al. Trichoderma spp. volatile organic compounds protect grapevine plants by activating defense-related processes against downy mildew. Physiol Plant. 2021;172:1950–1965. doi: 10.1111/ppl.13406. PubMed DOI PMC

Leal C, Richet N, Guise JF, Gramaje D, Armengol J, et al. Cultivar contributes to the beneficial effects of Bacillus subtilis PTA-271 and Trichoderma atroviride SC1 to protect grapevine against Neofusicoccum parvum. Front Microbiol. 2021;12:726132. doi: 10.3389/fmicb.2021.726132. PubMed DOI PMC

Lemoine F, Entfellner J-BD, Wilkinson E, Correia D, Felipe MD, et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature. 2018;556:452. doi: 10.1038/s41586-018-0043-0. PubMed DOI PMC

Li WC, Lin TC, Chen CL, Liu HC, Lin HN et al (2021) Complete genome sequences and genome-wide characterization of Trichoderma biocontrol agents provide new insights into their evolution and variation in genome organization, sexual development, and fungal-plant interactions. Microbiol Spectr 9(3):e00663-21 PubMed PMC

Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495. doi: 10.1093/nar/gkt1178. PubMed DOI PMC

López-Díaz TM, Santos JA, García-López ML, Otero A. Surface mycoflora of a Spanish fermented meat sausage and toxigenicity of Penicillium isolates. Int J Food Microbiol. 2001;68:69–74. doi: 10.1016/S0168-1605(01)00472-X. PubMed DOI

Lund F, Filtenborg O, Frisvad JC. Associated mycoflora of cheese. Food Microbiol. 1995;12:173–180. doi: 10.1016/S0740-0020(95)80094-8. DOI

Magistà D, Ferrara M, Del Nobile MA, Gammariello D, Conte A, et al. Penicillium salamii strain ITEM 15302: a new promising fungal starter for salami production. Int J Food Microbiol. 2016;231:33–41. doi: 10.1016/j.ijfoodmicro.2016.04.029. PubMed DOI

Magistà D, Susca A, Ferrara M, Logrieco AF, Perrone G. Penicillium species: crossroad between quality and safety of cured meat production. Curr Opin Food Sci. 2017;17:36–40. doi: 10.1016/j.cofs.2017.09.007. DOI

Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 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;38:4647–4654. doi: 10.1093/molbev/msab199. PubMed DOI PMC

Marin P, Palmero D, Jurado M (2014) Effect of solute and matric potential on growth rate of fungal species isolated from cheese. Int Dairy J 36(2):89–94. 10.1016/j.idairyj.2014.01.012

Marsberg A, Slippers B, Wingfield MJ, Gryzenhout M. Endophyte isolations from Syzygium cordatum and a eucalyptus clone (Myrtaceae) reveal new host and geographical reports for the Mycosphaerellaceae and Teratosphaeriaceae. Australas Plant Pathol. 2014;43:503–512. doi: 10.1007/s13313-014-0290-y. DOI

Martínez-Diz M, Díaz-Losada E, Andrés-Sodupe M, Bujanda R, Maldonado-González MM, et al. Field evaluation of biocontrol agents against black-foot and Petri diseases of grapevine. Pest Manag Sci. 2021;77(2):697–708. doi: 10.1002/ps.6064. PubMed DOI

Melén K, Krogh A, von Heijne G. Reliability measures for membrane protein topology prediction algorithms. J Mol Biol. 2003;327:735–744. doi: 10.1016/S0022-2836(03)00182-7. PubMed DOI

Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A. Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys. 2020;73:87–108. doi: 10.3897/mycokeys.73.53028. PubMed DOI PMC

Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018;34:i142–i150. doi: 10.1093/bioinformatics/bty266. PubMed DOI PMC

Minh BQ, Nguyen MAT, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 2013;30:1188–1195. doi: 10.1093/molbev/mst024. PubMed DOI PMC

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530–1534 Erratum in: Mol Biol Evol 37:2461 PubMed PMC

Mintzlaff H-J, Leistner L. Untersuchungen zur Selektion eines technologisch geeigneten und toxiologish unbedenklichen Schimmelpilz-stammes fur die Rohwurst-Herstellung. ZblVet Med B. 1972;19:291–300. PubMed

Munck IA, Livingston W, Lombard K, Luther T, Ostrofsky WD, Weimer J, Wyka S, Broders K. Extent and severity of caliciopsis canker in New England, USA: an emerging disease of eastern white pine (Pinus strobus L.) Forests. 2015;6:4360–4373. doi: 10.3390/f6114360. DOI

National Center for Biotechnology Information (NCBI) (2023) Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=63577 Accessed 07 Mar 2023

Nelson DR. The cytochrome p450 homepage. Hum Genomics. 2009;4:59–65. doi: 10.1186/1479-7364-4-1-59. PubMed DOI PMC

Nguyen TTT, Pangging M, Bangash NK, Lee HB. Five new records of the family Aspergillaceae in Korea, Aspergillus europaeus, A. pragensis, A. tennesseensis, Penicillium fluviserpens, and P. scabrosum. Mycobiology. 2020;48:81–94. doi: 10.1080/12298093.2020.1726563. PubMed DOI PMC

Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997;10:1–6. doi: 10.1093/protein/10.1.1. PubMed DOI

Owji H, Nezafat N, Negahdaripour M, Hajiebrahimi A, Ghasemi Y. A comprehensive review of signal peptides: structure, roles, and applications. Eur J Cell Biol. 2018;97:422–441. doi: 10.1016/j.ejcb.2018.06.003. PubMed DOI

Palmer JM, Stajich JE (2020) Funannotate v1.8.1: eukaryotic genome annotation. Zenodo. 10.5281/zenodo.4054262

Parussolo G, Bernardi AO, Garcia MV, Stefanello A, Silva TDS, et al. Fungi in air, raw materials and surface of dry fermented sausage produced in Brazil. Lwt. 2019;108:190–198. doi: 10.1016/j.lwt.2019.03.073. DOI

Pascoe IG, Smith IW, Dinh S-Q, Edwards J. Caliciopsis pleomorpha sp. nov. (Ascomycota: Coryneliales) causing a severe canker disease of Eucalyptus cladocalyx and other eucalypt species in Australia. Fungal Syst Evol. 2018;2:45–56. PubMed PMC

Peintner U, Geiger J, Pöder R. The mycobiota of speck, a traditional Tyrolean smoked and cured ham. J Food Prot. 2000;63:1399–1403. doi: 10.4315/0362-028X-63.10.1399. PubMed DOI

Perrone G, Samson RA, Frisvad JC, Susca A, Gunde-Cimerman N, et al. Penicillium salamii, a new species occurring during seasoning of dry-cured meat. Int J Food Microbiol. 2015;193:91–98. doi: 10.1016/j.ijfoodmicro.2014.10.023. PubMed DOI

Pertot I, Giovannini O, Benanchi M, Caffi T, Rossi V, et al. Combining biocontrol agents with different mechanisms of action in a strategy to control Botrytis cinerea on grapevine. J Crop Prot. 2017;97:85–93. doi: 10.1016/j.cropro.2017.01.010. DOI

Petersen C, Sørensen T, Nielsen MR, Sondergaard TE, Sørensen JL, et al. Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events. IMA Fungus. 2023;14:3. doi: 10.1186/s43008-023-00108-7. PubMed DOI PMC

Peterson SW, Jurjević Ž, Frisvad JC (2015) Expanding the species and chemical diversity of Penicillium section Cinnamopurpurea. PLoS ONE 10:e0121987–e0121987 PubMed PMC

Pozo MJ, Slezack-Deschaumes S, Dumas-Gaudot E, Gianinazzi S, Azcón-Aguilar C (2002) Plant defense responses induced by arbuscular mycorrhizal fungi. In: Mycorrhizal technology in agriculture, vol 1. Birkhäuser, Basel, p 103–111

Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21:i351–i358. doi: 10.1093/bioinformatics/bti1018. PubMed DOI

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc in Bioinformatics. 2020;70:102. doi: 10.1002/cpbi.102. PubMed DOI

Quaedvlieg W, Binder M, Groenewald JZ, Summerell BA, Carnegie AJ, et al. Introducing the consolidated species concept to resolve species in the Teratosphaeriaceae. Persoonia. 2014;33:1–40. doi: 10.3767/003158514X681981. PubMed DOI PMC

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33:W116–W120. doi: 10.1093/nar/gki442. PubMed DOI PMC

Ramos SO, Pérez CA. First report of Teratosphaeria pseudoeucalypti on eucalyptus hybrids in Argentina. Plant Dis. 2015;99:554–554. doi: 10.1094/PDIS-10-14-1087-PDN. DOI

Ramos-Pereira J, Mareze J, Patrinou E, Santos JA, López-Díaz TM. Polyphasic identification of Penicillium spp. isolated from Spanish semi-hard ripened cheeses. Food Microbiol. 2019;84:103253. doi: 10.1016/j.fm.2019.103253. PubMed DOI

Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 2014;42:D503–D509. doi: 10.1093/nar/gkt953. PubMed DOI PMC

Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: using the right methodology. Food Microbiol. 2019;81:51–62. doi: 10.1016/j.fm.2018.03.016. PubMed DOI

Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol. 2022;70:102236. doi: 10.1016/j.mib.2022.102236. PubMed DOI

Ropars J, Caron T, Lo YC, Bennetot B, Giraud T. La domestication des champignons Penicillium du fromage [The domestication of Penicillium cheese fungi] C R Biol. 2020;343:155–176. PubMed

Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M, et al. Domestication of the emblematic white cheese-making fungus Penicillium camemberti and its diversification into two varieties. Curr Biol. 2020;30:4441–4453.e4444. doi: 10.1016/j.cub.2020.08.082. PubMed DOI

Saier MH, Jr, Reddy VS, Tsu BV, Ahmed MS, Li C, et al. The transporter classification database (TCDB): recent advances. Nucleic Acids Res. 2016;44:D372–D379. doi: 10.1093/nar/gkv1103. PubMed DOI PMC

Savazzini F, Longa CMO, Pertot I, Gessler C. Real-time PCR for detection and quantification of the biocontrol agent Trichoderma atroviride strain SC1 in soil. J Microbiol Methods. 2008;73:185–194. doi: 10.1016/j.mimet.2008.02.004. PubMed DOI

Scaramuzza N, Diaferia C, Berni E. Monitoring the mycobiota of three plants manufacturing Culatello (a typical Italian meat product) Int J Food Microbiol. 2015;203:78–85. doi: 10.1016/j.ijfoodmicro.2015.02.034. PubMed DOI

Sharma P, Kumar V, Ramesh R, Saravanan K, Deep S, et al. Biocontrol genes from Trichoderma species: a review. Afr J Biotechnol. 2011;10(86):19898–19907.

Sharma S, Kour D, Rana KL, Dhiman A, Thakur S, et al. Recent advancement in white biotechnology through fungi. Cham: Springer; 2019. Trichoderma: biodiversity, ecological significances, and industrial applications; pp. 85–120.

Shi-Kunne X, Seidl MF, Faino L, Thomma BP (2015) Draft genome sequence of a strain of cosmopolitan fungus Trichoderma atroviride. Genome Announc 3(3):10–1128 PubMed PMC

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–3212. doi: 10.1093/bioinformatics/btv351. PubMed DOI

Smit AFA, Hubley R, Green P (1996–2010) RepeatMasker Open-3.0. <http://www.repeatmasker.org>.

Sood M, Kapoor D, Kumar V, Sheteiwy MS, Ramakrishnan M, et al. Trichoderma: the “secrets” of a multitalented biocontrol agent. Plants. 2020;9:762. doi: 10.3390/plants9060762. PubMed DOI PMC

Sørensen LM, Jacobsen T, Nielsen PV, Frisvad JC, Koch AG. Mycobiota in the processing areas of two different meat products. Int J Food Microbiol. 2008;124:58–64. doi: 10.1016/j.ijfoodmicro.2008.02.019. PubMed DOI

Soria S, Alonso R, Bettucci L, Lupo S. First report of Teratosphaeria pseudoeucalypti in Uruguay. Aust Plant Dis Notes. 2014;9:146. doi: 10.1007/s13314-014-0146-x. DOI

Steenwyk JL, Shen XX, Lind AL, Goldman GH, Rokas A. A robust phylogenomic time tree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. Mbio. 2019;10:e00925–e1019. doi: 10.1128/mBio.00925-19. PubMed DOI PMC

Tamang JP, Shin DH, Jung SJ, Chae SW. Functional properties of microorganisms in fermented foods. Front Microbiol. 2016;7:578. doi: 10.3389/fmicb.2016.00578. PubMed DOI PMC

Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022–3027. doi: 10.1093/molbev/msab120. PubMed DOI PMC

Taole M, Bihon W, Wingfield BD, Wingfield MJ, Burgess TI. Multiple introductions from multiple sources: invasion patterns for an important Eucalyptus leaf pathogen. Ecol Evol. 2015;5:4210–4220. doi: 10.1002/ece3.1693. PubMed DOI PMC

Thom C (1906) Fungi in cheese ripening: camembert and roquefort. US Department of Agriculture, Bureau of Animal Industry—Bulletin 82:1–39

Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232–W235. doi: 10.1093/nar/gkw256. PubMed DOI PMC

Tronsmo A. Biological and integrated controls of Botrytis cinerea on apple with Trichoderma harzianum. Biol Control. 1991;1:59–62. doi: 10.1016/1049-9644(91)90102-6. DOI

Vinale F, Sivasithamparam K. Beneficial effects of Trichoderma secondary metabolites on crops. Phytother Res. 2020;34(11):2835–2842. doi: 10.1002/ptr.6728. PubMed DOI

Vinale F, Sivasithamparam K, Ghisalberti EL, Marra R, Woo SL, et al. Trichoderma–plant–pathogen interactions. Soil Biol Biochem. 2008;40:1–10. doi: 10.1016/j.soilbio.2007.07.002. DOI

Visagie CM, Houbraken J, Frisvad JC, et al. Identification and nomenclature of the genus Penicillium. Stud Mycol. 2014;78:343–371. doi: 10.1016/j.simyco.2014.09.001. PubMed DOI PMC

White T, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protoc Guid Methods Appl. 1990;18:315–322.

Wingfield BD, Liu M, Nguyen HD, Lane FA, Morgan SW, et al. Nine draft genome sequences of Claviceps purpurea s. lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans . IMA Fungus. 2018;9:401. doi: 10.5598/imafungus.2018.09.02.10. PubMed DOI PMC

Wingfield BD, Fourie A, Simpson MC, Bushula-Njah VS, Aylward J, et al. IMA genome-F 11 Draft genome sequences of Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis and genome annotation for Ceratocystis fimbriata. IMA Fungus. 2019;10:13. doi: 10.1186/s43008-019-0013-7. PubMed DOI PMC

Wood AR, Damm U, van der Linde EJ, Groenewald JZ, Cheewangkoon R, Crous PW. Finding the missing link: resolving the Coryneliomycetidae within Eurotiomycetes. Persoonia. 2016;37:37. doi: 10.3767/003158516X689800. PubMed DOI PMC

Wu G, Jurick Ii WM, Lichtner FJ, Peng H, Yin G, et al. Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay. PeerJ. 2019;7:e6170. doi: 10.7717/peerj.6170. PubMed DOI PMC

Yin Y, Mao X, Yang J, Chen X, Mao F, et al. dbCAN: A web resource for automated carbohydrate- active enzyme annotation. Nucleic Acids Res. 2012;40:445–451. doi: 10.1093/nar/gks479. PubMed DOI PMC

Zhang Z, Wood WI. A profile hidden Markov model for signal peptides generated by HMMER. Bioinformatics. 2003;19:307–308. doi: 10.1093/bioinformatics/19.2.307. PubMed DOI

Zhou Y, Wang Y, Chen K, Wu Y, Hu J, et al. Near-complete genomes of two Trichoderma species: a resource for biological control of plant pathogens. Mol Plant-Microbe Interact. 2020;33:1036–1039. doi: 10.1094/MPMI-03-20-0076-A. PubMed DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...