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Fungal Pathogen in Digital Age: Review on Current State and Trend of Comparative Genomics Studies of Pathogenic Fungi


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Alastruey-Izquierdo A., Alcazar-Fuoli L., Cuenca-Estrella M.: Antifungal susceptibility profile of cryptic species of Aspergillus. Mycopathologia, 178, 427–433 (2014) Alastruey-Izquierdo A. Alcazar-Fuoli L. Cuenca-Estrella M. : Antifungal susceptibility profile of cryptic species of Aspergillus . Mycopathologia , 178 , 427 433 ( 2014 ) Search in Google Scholar

Amselem J. & Fournier E. et al.: Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 7, e1002230 (2011) Amselem J. & Fournier E. .: Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea . PLoS Genet . 7 , e1002230 ( 2011 ) Search in Google Scholar

Basenko E. & Hertz-Fowler C. et al.: FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J. Fungi, 4, 39 (2018) Basenko E. & Hertz-Fowler C. .: FungiDB: an integrated bioinformatic resource for fungi and oomycetes . J. Fungi , 4 , 39 ( 2018 ) Search in Google Scholar

Bellemain E., Carlsen T., Brochmann C., Coissac E., Taberlet P., Kauserud H.: ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10, 189 (2010) Bellemain E. Carlsen T. Brochmann C. Coissac E. Taberlet P. Kauserud H. : ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases . BMC Microbiol . 10 , 189 ( 2010 ) Search in Google Scholar

Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Ostell J., Pruitt K.D., Sayers E.W.: GenBank. Nucleic Acids Res. 46, D41–47 (2017) Benson D.A. Cavanaugh M. Clark K. Karsch-Mizrachi I. Ostell J. Pruitt K.D. Sayers E.W. : GenBank . Nucleic Acids Res . 46 , D41–47 ( 2017 ) Search in Google Scholar

Bernardi G., Wiley E.O., Mansour H., Miller M.R., Orti G., Haussler D., O’Brien S.J., Ryder O.A., Venkatesh B.: The fishes of genome 10K. Mar. Genom. 7, 3–6 (2012) Bernardi G. Wiley E.O. Mansour H. Miller M.R. Orti G. Haussler D. O’Brien S.J. Ryder O.A. Venkatesh B. : The fishes of genome 10K . Mar. Genom . 7 , 3 6 ( 2012 ) Search in Google Scholar

Brown G.D., Denning D.W., Gow N.A.R., Levitz S.M., Netea M.G., White T.C.: Hidden killers: human fungal infections. Sci. Transl. Med. 4, 165rv13–165rv13 (2012) Brown G.D. Denning D.W. Gow N.A.R. Levitz S.M. Netea M.G. White T.C. : Hidden killers: human fungal infections . Sci. Transl. Med . 4 , 165rv13–165rv13 ( 2012 ) Search in Google Scholar

Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L.: BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009) Camacho C. Coulouris G. Avagyan V. Ma N. Papadopoulos J. Bealer K. Madden T.L. : BLAST+: architecture and applications . BMC Bioinform . 10 , 421 ( 2009 ) Search in Google Scholar

https://www.cdc.gov/fungal/diseases/index.html CDC (2019): Types of Fungal Diseases. Centers for Disease Control and Prevention, (12.09.2023) https://www.cdc.gov/fungal/diseases/index.html CDC ( 2019 ): Types of Fungal Diseases . Centers for Disease Control and Prevention , (12.09.2023) Search in Google Scholar

Chen H., King R., Smith D. Bayon C., Ashfield T., Torriani S., Kanyuka K., Hammond-Kosack K., Bieri S., Rudd J.: Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen. BMC Biol, 21, 24 (2023) Chen H. King R. Smith D. Bayon C. Ashfield T. Torriani S. Kanyuka K. Hammond-Kosack K. Bieri S. Rudd J. : Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen . BMC Biol , 21 , 24 ( 2023 ) Search in Google Scholar

Chybowska A.D., Childers D.S., Farrer R.A.: Nine things genomics can tell us about Candida auris. Front. Genet. 11, 351 (2020) Chybowska A.D. Childers D.S. Farrer R.A. : Nine things genomics can tell us about Candida auris . Front. Genet . 11 , 351 ( 2020 ) Search in Google Scholar

Corley R.H.V. & Tinker P.B.: Vegetative propagation and biotechnology (in) The oil palm, Ed. R.H.V. Corley, P.B. Tinker, Wiley-Blackwell, 201–215 (2003) Corley R.H.V. & Tinker P.B. : Vegetative propagation and biotechnology (in) The oil palm , Ed. Corley R.H.V. Tinker P.B. , Wiley-Blackwell , 201 215 ( 2003 ) Search in Google Scholar

Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L.: Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499–510 (2011) Davey J.W. Hohenlohe P.A. Etter P.D. Boone J.Q. Catchen J.M. Blaxter M.L. : Genome-wide genetic marker discovery and genotyping using next-generation sequencing . Nat. Rev. Genet . 12 , 499 510 ( 2011 ) Search in Google Scholar

de Sena Brandine G., Smith A.D.: Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research, 8, 1874 (2021) de Sena Brandine G. Smith A.D. : Falco: high-speed FastQC emulation for quality control of sequencing data . F1000Research , 8 , 1874 ( 2021 ) Search in Google Scholar

Dean R. & Foster G.D. et al.: The top 10 fungal pathogens in molecular plant pathology. Mol. Plant Pathol. 13, 414–430 (2012) Dean R. & Foster G.D. .: The top 10 fungal pathogens in molecular plant pathology . Mol. Plant Pathol . 13 , 414 430 ( 2012 ) Search in Google Scholar

Dean R.A. & Birren B.W. et al.: The genome sequence of the rice blast fungus Magnaporthe grisea. Nature, 434, 980–986 (2005) Dean R.A. & Birren B.W. .: The genome sequence of the rice blast fungus Magnaporthe grisea . Nature , 434 , 980 986 ( 2005 ) Search in Google Scholar

Demir E., Babur O., Dogrusoz U., Gursoy A., Nisanci G., Cetin-Atalay R., Orzturk M.: Patika: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics, 18, 996–1003 (2002) Demir E. Babur O. Dogrusoz U. Gursoy A. Nisanci G. Cetin-Atalay R. Orzturk M. : Patika: an integrated visual environment for collaborative construction and analysis of cellular pathways . Bioinformatics , 18 , 996 1003 ( 2002 ) Search in Google Scholar

Dickman M.B., de Figueiredo P.: Comparative pathobiology of fungal pathogens of plants and animals. PLoS Pathog. 7, e1002324 (2011) Dickman M.B. de Figueiredo P. : Comparative pathobiology of fungal pathogens of plants and animals . PLoS Pathog . 7 , e1002324 ( 2011 ) Search in Google Scholar

dos Santos R.A.C., Steenwyk J.L., Rivero-Menendez O., Mead M.E., Silva L.P., Bastos R.W., Alastruey-Izquierdo A., Goldman G.H., Rokas A.: Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis. Front. Genet. 11, 459 (2020) dos Santos R.A.C. Steenwyk J.L. Rivero-Menendez O. Mead M.E. Silva L.P. Bastos R.W. Alastruey-Izquierdo A. Goldman G.H. Rokas A. : Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis . Front. Genet . 11 , 459 ( 2020 ) Search in Google Scholar

Duplessis S. & Chiu R. et al.: Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc. Natl. Acad. Sci. 108, 9166–71 (2011) Duplessis S. & Chiu R. .: Obligate biotrophy features unraveled by the genomic analysis of rust fungi . Proc. Natl. Acad. Sci . 108 , 9166 71 ( 2011 ) Search in Google Scholar

Edgar R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004) Edgar R.C. : MUSCLE: multiple sequence alignment with high accuracy and high throughput . Nucleic Acids Res . 32 , 1792 1797 ( 2004 ) Search in Google Scholar

Fukuda A., Kodama Y., Mashima J., Fujisawa T., Ogasawara O.: DDBJ update: streamlining submission and access of human data. Nucleic Acids Res. 49, D71–75 (2020) Fukuda A. Kodama Y. Mashima J. Fujisawa T. Ogasawara O. : DDBJ update: streamlining submission and access of human data . Nucleic Acids Res . 49 , D71–75 ( 2020 ) Search in Google Scholar

https://www.broadinstitute.org/fungal-genome-initiative Broad Institute (2008): Fungal Genomics, (25.09.2023) https://www.broadinstitute.org/fungal-genome-initiative Broad Institute ( 2008 ): Fungal Genomics , (25.09.2023) Search in Google Scholar

Guirao-Abad J.P., Weichert M., Luengo-Gil G., Sze Wah Wong S., Aimanianda V., Grisham C., Malev N., Reddy S., Woollett L., Askew D.S.: Pleiotropic effects of the P5-type ATPase SpfA on stress response networks contribute to virulence in the pathogenic mold Aspergillus fumigatus. MBio, 12, 10–1123 (2021) Guirao-Abad J.P. Weichert M. Luengo-Gil G. Sze Wah Wong S. Aimanianda V. Grisham C. Malev N. Reddy S. Woollett L. Askew D.S. : Pleiotropic effects of the P5-type ATPase SpfA on stress response networks contribute to virulence in the pathogenic mold Aspergillus fumigatus . MBio , 12 , 10 1123 ( 2021 ) Search in Google Scholar

Gupta A.K., Jain H.C., Lynde C.W., MacDonald P., Cooper E.A., Summerbell R.C.: Prevalence and epidemiology of onychomycosis in patients visiting physicians’ offices: a multicenter Canadian survey of 15,000 patients. J. Am. Acad. Dermatol. 43, 244–248 (2000) Gupta A.K. Jain H.C. Lynde C.W. MacDonald P. Cooper E.A. Summerbell R.C. : Prevalence and epidemiology of onychomycosis in patients visiting physicians’ offices: a multicenter Canadian survey of 15,000 patients . J. Am. Acad. Dermatol . 43 , 244 248 ( 2000 ) Search in Google Scholar

Hall B.G.: Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 30(5), 1229–1235 (2013) Hall B.G. : Building phylogenetic trees from molecular data with MEGA . Mol Biol Evol 30 ( 5 ), 1229 1235 ( 2013 ) Search in Google Scholar

Hamer J.E., Holden D.W.: Linking approaches in the study of fungal pathogenesis: a commentary. Fungal. Genet. Biol. 21, 11–16 (1997) Hamer J.E. Holden D.W. : Linking approaches in the study of fungal pathogenesis: a commentary . Fungal. Genet. Biol . 21 , 11 16 ( 1997 ) Search in Google Scholar

Hariharan G., Prasannath K.: Recent advances in molecular diagnostics of fungal plant pathogens: a mini review. Front. Cell. Infect. Microbiol. 10, 600234 (2021) Hariharan G. Prasannath K. : Recent advances in molecular diagnostics of fungal plant pathogens: a mini review . Front. Cell. Infect. Microbiol . 10 , 600234 ( 2021 ) Search in Google Scholar

Heitman J.: Microbial pathogens in the fungal kingdom. Fungal Biol. Rev. 25, 48–60 (2011) Heitman J. : Microbial pathogens in the fungal kingdom . Fungal Biol. Rev . 25 , 48 60 ( 2011 ) Search in Google Scholar

Hingamp P., van den Broek A.E., Stoesser G., Baker W.: The EMBL nucleotide sequence database: contributing and accessing data. Mol. Biotechnol. 12, 255–268 (1999) Hingamp P. van den Broek A.E. Stoesser G. Baker W. : The EMBL nucleotide sequence database: contributing and accessing data . Mol. Biotechnol . 12 , 255 268 ( 1999 ) Search in Google Scholar

Howe K.L. & Flicek P. et al.: Ensembl 2021. Nucleic Acids Res. 49, D884–D891 (2020) Howe K.L. & Flicek P. .: Ensembl 2021 . Nucleic Acids Res . 49 , D884–D891 ( 2020 ) Search in Google Scholar

Hu Z.: Using VisANT to analyze networks. Curr. Protoc. Bioinf. 45, 8–8 (2014) Hu Z. : Using VisANT to analyze networks . Curr. Protoc. Bioinf . 45 , 8 8 ( 2014 ) Search in Google Scholar

Hushiarian R., Yusof N.A., Dutse S.W: Detection and control of Ganoderma boninense: Strategies and perspectives. Springer-Plus, 2, 555 (2013) Hushiarian R. Yusof N.A. Dutse S.W : Detection and control of Ganoderma boninense: Strategies and perspectives . Springer-Plus , 2 , 555 ( 2013 ) Search in Google Scholar

Jain A., Singhal N., Kumar M.: AFRbase: a database of protein mutations responsible for antifungal resistance. Bioinformatics, 39, 11 (2023) Jain A. Singhal N. Kumar M. : AFRbase: a database of protein mutations responsible for antifungal resistance . Bioinformatics , 39 , 11 ( 2023 ) Search in Google Scholar

http://www.glycopedia.eu/IMG/pdf/the_plant_cell_walls.pdf Joseleau J.P., Pérez S. (2016) The Plant Cell Walls: complex polysaccharide nano-composites, (13.09.2023) http://www.glycopedia.eu/IMG/pdf/the_plant_cell_walls.pdf Joseleau J.P. Pérez S. ( 2016 ) The Plant Cell Walls: complex polysaccharide nano-composites , (13.09.2023) Search in Google Scholar

Kaczmarek A.M., King K.M., West J.S., Stevens M., Sparkes D., Dickinson M.J.: A loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of airborne inoculum of Uromyces betae (Sugar Beet Rust). Plant Dis. 103, 417–421 (2019) Kaczmarek A.M. King K.M. West J.S. Stevens M. Sparkes D. Dickinson M.J. : A loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of airborne inoculum of Uromyces betae (Sugar Beet Rust) . Plant Dis . 103 , 417 421 ( 2019 ) Search in Google Scholar

Kämper J. & Birren B.W. et al.: Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 444, 97–101 (2006) Kämper J. & Birren B.W. .: Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis . Nature , 444 , 97 101 ( 2006 ) Search in Google Scholar

Katoh K.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002) Katoh K. : MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform . Nucleic Acids Res . 30 , 3059 3066 ( 2002 ) Search in Google Scholar

King R., Brown N.A., Urban M., Hammond-Kosack K.E.: Intergenome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genom. 19, 1–19 (2018) King R. Brown N.A. Urban M. Hammond-Kosack K.E. : Intergenome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum . BMC Genom . 19 , 1 19 ( 2018 ) Search in Google Scholar

Koepfli K.P., Paten B., O’Brien S.J.: The genome 10K project: a way forward. Annu. Rev. Anim. Biosci. 3, 57–111 (2015) Koepfli K.P. Paten B. O’Brien S.J. : The genome 10K project: a way forward . Annu. Rev. Anim. Biosci . 3 , 57 111 ( 2015 ) Search in Google Scholar

Kozel T.R., Wickes B.: Fungal diagnostics. Cold Spring Harbor Perspect. Med. 4(4), a019299 (2014) Kozel T.R. Wickes B. : Fungal diagnostics . Cold Spring Harbor Perspect. Med . 4 ( 4 ) , a019299 ( 2014 ) Search in Google Scholar

Lombard V., Golaconda Ramulu H, Drula E., Coutinho P.M., Henrissat B.: The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2013) Lombard V. Golaconda Ramulu H Drula E. Coutinho P.M. Henrissat B. : The carbohydrate-active enzymes database (CAZy) in 2013 . Nucleic Acids Res . 42 , D490–D495 ( 2013 ) Search in Google Scholar

Lu T., Yao B., Zhang C.: DFVF: database of fungal virulence factors. Database, 2012, bas032 (2012) Lu T. Yao B. Zhang C. : DFVF: database of fungal virulence factors . Database , 2012 , bas032 ( 2012 ) Search in Google Scholar

Dieckmann M.A., Beyvers S., Beyvers S., Nkouamedjo-Fankep R.C., Hanel P.H., Jelonek L., Blom J., Goesmann A.: EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Nucleic Acids Res. 49, W185–W192 (2021) Dieckmann M.A. Beyvers S. Beyvers S. Nkouamedjo-Fankep R.C. Hanel P.H. Jelonek L. Blom J. Goesmann A. : EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure . Nucleic Acids Res . 49 , W185–W192 ( 2021 ) Search in Google Scholar

Moran G.P., Coleman D.C., Sullivan D.J.: Comparative genomics and the evolution of pathogenicity in human pathogenic fungi. Eukaryotic Cell, 10, 34–42 (2011) Moran G.P. Coleman D.C. Sullivan D.J. : Comparative genomics and the evolution of pathogenicity in human pathogenic fungi . Eukaryotic Cell , 10 , 34 42 ( 2011 ) Search in Google Scholar

Nash A., Sewell T., Farrer R.A., Abdolrasouli A., Shelton J.M.G., Fisher M.C. & Rhodes J.: MARDy: Mycology Antifungal Resistance Database. Bioinformatics, 34, 3233–3234 (2018) Nash A. Sewell T. Farrer R.A. Abdolrasouli A. Shelton J.M.G. Fisher M.C. & Rhodes J. : MARDy: Mycology Antifungal Resistance Database . Bioinformatics , 34 , 3233 3234 ( 2018 ) Search in Google Scholar

Okonechnikov K., Golosova O., Fursov M.: Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics, 28, 1166–1167 (2012) Okonechnikov K. Golosova O. Fursov M. : Unipro UGENE: a unified bioinformatics toolkit . Bioinformatics , 28 , 1166 1167 ( 2012 ) Search in Google Scholar

Nikitin, A., Egorov, S., Daraselia, N., & Mazo, I. (2003). Pathway studio--the analysis and navigation of molecular networks. Bioinformatics (Oxford, England), 19(16), 2155–2157. https://doi.org/10.1093/bioinformatics/btg290 Nikitin A. Egorov S. Daraselia N. & Mazo I. ( 2003 ). Pathway studio--the analysis and navigation of molecular networks . Bioinformatics (Oxford, England) , 19 ( 16 ), 2155 2157 . https://doi.org/ 10.1093/bioinformatics/btg290 Open DOISearch in Google Scholar

Pierre M.J. & Ksenia V.K.: Distinct genomic context predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics, iyae012 (2024). Advanced online ublication. Pierre M.J. & Ksenia V.K. : Distinct genomic context predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae . Genetics , iyae012 ( 2024 ) . Advanced online ublication. Search in Google Scholar

Prakash H., Rudramurthy S.M., Gandham P.S., Ghosh A.K., Kumar M.M., Badapanda C., Chakrabarti A.: Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. BMC Genom. 18, 1–13 (2017) Prakash H. Rudramurthy S.M. Gandham P.S. Ghosh A.K. Kumar M.M. Badapanda C. Chakrabarti A. : Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales . BMC Genom . 18 , 1 13 ( 2017 ) Search in Google Scholar

Ramzi A.B., Che Me M.L., Ruslan U.S., Baharum S.N., Nor Muhammad N.A.: Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ, 7, e8065 (2019) Ramzi A.B. Che Me M.L. Ruslan U.S. Baharum S.N. Nor Muhammad N.A. : Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis . PeerJ , 7 , e8065 ( 2019 ) Search in Google Scholar

Retief J.D.: Phylogenetic analysis using PHYLIP. Bioinf. Method. Protoc. 243–258 (2000) Retief J.D. : Phylogenetic analysis using PHYLIP . Bioinf. Method. Protoc . 243 258 ( 2000 ) Search in Google Scholar

Sexton A.C., Howlett B.J.: Parallels in fungal pathogenesis on plant and animal hosts. Eukaryotic Cell, 5, 1941–1949 (2019) Sexton A.C. Howlett B.J. : Parallels in fungal pathogenesis on plant and animal hosts . Eukaryotic Cell , 5 , 1941 1949 ( 2019 ) Search in Google Scholar

Seyedmousavi S., Guillot J., Arné P., de Hoog G.S., Mouton J.W., Melchers W.J.G., Verweij P.E.: Aspergillus and aspergilloses in wild and domestic animals: a global health concern with parallels to human disease. Med. Mycol. 53, 765–797 (2015) Seyedmousavi S. Guillot J. Arné P. de Hoog G.S. Mouton J.W. Melchers W.J.G. Verweij P.E. : Aspergillus and aspergilloses in wild and domestic animals: a global health concern with parallels to human disease . Med. Mycol . 53 , 765 797 ( 2015 ) Search in Google Scholar

Shannon P.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome. Res. 13, 2498–2504 (2003) Shannon P. : Cytoscape: a software environment for integrated models of biomolecular interaction networks . Genome. Res . 13 , 2498 2504 ( 2003 ) Search in Google Scholar

Sharon A., Shlezinger N.: Fungi infecting plants and animals: killers, non-killers, and cell death. PLoS Pathog. 9, e1003517 (2013) Sharon A. Shlezinger N. : Fungi infecting plants and animals: killers, non-killers, and cell death . PLoS Pathog . 9 , e1003517 ( 2013 ) Search in Google Scholar

Shi-Kunne X., van Kooten M., Depotter J.R.L., Thomma B.P., Seidl M.F.: The genome of the fungal pathogen Verticillium dahliae reveals extensive bacterial to fungal gene transfer. Genome Biol. Evol. 11, 855–868 (2019) Shi-Kunne X. van Kooten M. Depotter J.R.L. Thomma B.P. Seidl M.F. : The genome of the fungal pathogen Verticillium dahliae reveals extensive bacterial to fungal gene transfer . Genome Biol. Evol . 11 , 855 868 ( 2019 ) Search in Google Scholar

Thompson J.D., Gibson T.J., Higgins D.G.: Multiple sequence alignment using ClustalW and ClustalX. Current Protoc. Bioinf. 2–3 (2002) Thompson J.D. Gibson T.J. Higgins D.G. : Multiple sequence alignment using ClustalW and ClustalX . Current Protoc. Bioinf . 2 3 ( 2002 ) Search in Google Scholar

Tissot F., Lamoth F., Hauser P.M., Orasch C., Flückiger U., Siegemund M., Zimmerli S., Calandra T., Bille J., Eggimann P., Marchetti O.: Fungal Infection Network of Switzerland (FUNGINOS). β-glucan antigenemia anticipates diagnosis of blood culture-negative intraabdominal candidiasis. Am J Respir Crit Care Med. 188, 1100–9 (2013) Tissot F. Lamoth F. Hauser P.M. Orasch C. Flückiger U. Siegemund M. Zimmerli S. Calandra T. Bille J. Eggimann P. Marchetti O. : Fungal Infection Network of Switzerland (FUNGINOS). β-glucan antigenemia anticipates diagnosis of blood culture-negative intraabdominal candidiasis . Am J Respir Crit Care Med . 188 , 1100 9 ( 2013 ) Search in Google Scholar

Urban M. & Hammond-Kosack K.E. et al.: PHI-base: the pathogen-host interactions database. Nucleic Acid Res. 48, D613–D620 (2020) Urban M. & Hammond-Kosack K.E. .: PHI-base: the pathogen-host interactions database . Nucleic Acid Res . 48 , D613–D620 ( 2020 ) Search in Google Scholar

van Dam P., de Sain M., Ter Horst A., van der Gragt M., Rep M.: Use of comparative genomics-based markers for discrimination of host specificity in Fusarium oxysporum. Appl. Environ. Microbiol. 84, e01868–17 (2018) van Dam P. de Sain M. Ter Horst A. van der Gragt M. Rep M. : Use of comparative genomics-based markers for discrimination of host specificity in Fusarium oxysporum . Appl. Environ. Microbiol . 84 , e01868–17 ( 2018 ) Search in Google Scholar

van der Does H.C., Rep M.: Virulence genes and the evolution of host specificity in plant-pathogenic fungi. Mol. Plant-Microbe Interact. 20, 1175–1182 (2007) van der Does H.C. Rep M. : Virulence genes and the evolution of host specificity in plant-pathogenic fungi . Mol. Plant-Microbe Interact . 20 , 1175 1182 ( 2007 ) Search in Google Scholar

Walker T.S., Bais H.P., Déziel E., Schweizer H.P., Rahme L.G., Fall R., Vivanco J.M.: Pseudomonas aeruginosa-plant root interactions. Pathogenicity, biofilm formation, and root exudation. Plant Physiol. 134, 320–331 (2003) Walker T.S. Bais H.P. Déziel E. Schweizer H.P. Rahme L.G. Fall R. Vivanco J.M. : Pseudomonas aeruginosa-plant root interactions. Pathogenicity, biofilm formation, and root exudation . Plant Physiol . 134 , 320 331 ( 2003 ) Search in Google Scholar

Weber M., Schaer J., Walther G., Kaerger K., Steinmann J., Rath P.M., Spiess B., Buchheidt D., Hamprecht A., & Kurzai O.: FunResDB-A web resource for genotypic susceptibility testing of Aspergillus fumigatus. Medical mycology, 56, 117–120 (2018) Weber M. Schaer J. Walther G. Kaerger K. Steinmann J. Rath P.M. Spiess B. Buchheidt D. Hamprecht A. & Kurzai O. : FunResDB-A web resource for genotypic susceptibility testing of Aspergillus fumigatus . Medical mycology , 56 , 117 120 ( 2018 ) Search in Google Scholar

Wei L., Liu Y., Dubchak I., Shon J., Park J.: Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inf. 35, 142–150 (2002) Wei L. Liu Y. Dubchak I. Shon J. Park J. : Comparative genomics approaches to study organism similarities and differences . J. Biomed. Inf . 35 , 142 150 ( 2002 ) Search in Google Scholar

Fang W., Wu J., Cheng M., Zhu X., Du M., Chen C., Liao W., Zhi K., Pan W.: Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci. 30, 42 (2023) Fang W. Wu J. Cheng M. Zhu X. Du M. Chen C. Liao W. Zhi K. Pan W. : Diagnosis of invasive fungal infections: challenges and recent developments . J Biomed Sci . 30 , 42 ( 2023 ) Search in Google Scholar

https://www.who.int/publications/i/item/9789240060241 World Health Organization (2022): WHO fungal priority pathogens list to guide research and public health action (11.02.2024) https://www.who.int/publications/i/item/9789240060241 World Health Organization ( 2022 ): WHO fungal priority pathogens list to guide research and public health action (11.02.2024) Search in Google Scholar

Yandell M., Ence D.: A beginner’s guide to eukaryotic genome annotation. Nat. Rev. Genet. 13, 329–342 (2012) Yandell M. Ence D. : A beginner’s guide to eukaryotic genome annotation . Nat. Rev. Genet . 13 , 329 342 ( 2012 ) Search in Google Scholar

Yu CH, Sephton-Clark P, Tenor JL, Toffaletti DL, Giamberardino C, Haverkamp M., Cuomo C.A., Perfect J.R.: Gene expression of diverse Cryptococcus isolates during infection of the human central nervous system. Mbio, 12, e02313–21 (2021) Yu CH Sephton-Clark P Tenor JL Toffaletti DL Giamberardino C Haverkamp M. Cuomo C.A. Perfect J.R. : Gene expression of diverse Cryptococcus isolates during infection of the human central nervous system . Mbio , 12 , e02313–21 ( 2021 ) Search in Google Scholar

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Life Sciences, Microbiology and Virology