Skip to main content

Introduction: Overview of Fungal Genomics

  • Protocol
  • First Online:
Fungal Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1775))

Abstract

Genome sequences and postgenomic tools have had a major impact on fungal research. When the first fungal genome sequences became available it became clear how much more complex fungal biology was than had been previously assumed. Since then an increasing number of genomes have become available enabling detailed comparative studies, especially when combined with postgenomic tools such as transcriptomics and proteomics. This chapter provides an overview and current state of fungal genomics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:546–547

    Article  CAS  PubMed  Google Scholar 

  2. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422(6934):859–868

    Article  CAS  PubMed  Google Scholar 

  3. Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Guldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuveglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Segurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7(8):e1002230. https://doi.org/10.1371/journal.pgen.1002230

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE (2012) The Genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet 8(11):e1003088. https://doi.org/10.1371/journal.pgen.1003088

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, Labutti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen dothideomycetes fungi. PLoS Pathog 8(12):e1003037. https://doi.org/10.1371/journal.ppat.1003037

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Gorecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kues U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Duenas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089):1715–1719. https://doi.org/10.1126/science.1221748

    Article  PubMed  CAS  Google Scholar 

  7. Peng M, Dilokpirnol A, Makela MR, Hilden K, Bervoets S, Riley R, Grigoriev IV, Hainaut M, Henrissat B, de Vries RP, Granchi Z (2017) The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi. J Biotechnol 246:1–3

    Article  CAS  PubMed  Google Scholar 

  8. Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR (2014) Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 78(4):614–649. https://doi.org/10.1128/MMBR.00035-14

    Article  PubMed  PubMed Central  Google Scholar 

  9. Acton E, Lee AHY, Zhao PJ, Flibotte S, Neira M, Sinha S, Chiang J, Flaherty P, Nislow C, Giaever G (2017) Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. Open Biol 7(6). https://doi.org/10.1098/rsob.160330

    Article  PubMed  PubMed Central  Google Scholar 

  10. de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram O, Benocci T, Braus-Stromeyer SA, Caldana C, Canovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damasio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hilden KS, Hope R, Hossain A, Karabika E, Karaffa L, Karanyi Z, Krasevec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Makela MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnar AP, Mule G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramon A, Rauscher S, Record E, Riano-Pachon DM, Robert V, Rohrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sandor E, Sanguinetti M, Schutze T, Sepcic K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pocsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18(1):28. https://doi.org/10.1186/s13059-017-1151-0

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Klaubauf S, Narang HM, Post H, Zhou M, Brunner K, Mach-Aigner AR, Mach RL, Heck AJ, Altelaar AF, de Vries RP (2014) Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genet Biol 72:73–81. https://doi.org/10.1016/j.fgb.2014.07.007

    Article  PubMed  CAS  Google Scholar 

  12. Peng M, Aguilar-Pontes MV, Hainaut M, Henrissat B, Hildén K, Mäkelä MR, de Vries RP (2017) Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes. Fungal Genet Biol. https://doi.org/10.1016/j.fgb.2017.08.001

  13. Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TB (2017) Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res 45(D1):D446–D456. https://doi.org/10.1093/nar/gkw992

    Article  PubMed  CAS  Google Scholar 

  14. Rossman AY (1995) A strategy for an all-taxa inventory of fungal biodiversity. In: Peng C, Chou CH (eds) Biodiversity and terrestrial ecosystems. Academia Sinica, Taiwan, pp 169–194

    Google Scholar 

  15. Hittinger CT, Rokas A, Bai FY, Boekhout T, Goncalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP (2015) Genomics and the making of yeast biodiversity. Curr Opin Genet Dev 35:100–109. https://doi.org/10.1016/j.gde.2015.10.008

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42(Database issue):D699–D704. https://doi.org/10.1093/nar/gkt1183

    Article  CAS  PubMed  Google Scholar 

  17. Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res 44(D1):D698–D702. https://doi.org/10.1093/nar/gkv1250

    Article  PubMed  CAS  Google Scholar 

  18. Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G (2017) The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res 45(D1):D592–D596. https://doi.org/10.1093/nar/gkw924

    Article  PubMed  CAS  Google Scholar 

  19. Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40(Database issue):D675–D681. https://doi.org/10.1093/nar/gkr918

    Article  PubMed  CAS  Google Scholar 

  20. Park J, Park B, Jung K, Jang S, Yu K, Choi J, Kong S, Park J, Kim S, Kim H, Kim S, Kim JF, Blair JE, Lee K, Kang S, Lee YH (2008) CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res 36(Database issue):D562–D571. https://doi.org/10.1093/nar/gkm758

    Article  PubMed  CAS  Google Scholar 

  21. Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res 44(D1):D574–D580. https://doi.org/10.1093/nar/gkv1209

    Article  PubMed  CAS  Google Scholar 

  22. Robbertse B, Tatusova T (2011) Fungal genome resources at NCBI. Mycology 2(3):142–160

    PubMed  PubMed Central  CAS  Google Scholar 

  23. Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M (2017) The Fungal Tree of Life: from molecular systematics to genome-scale phylogenies. Microbiol Spectr 5(5). https://doi.org/10.1128/microbiolspec.FUNK-0053-2016

  24. Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL (2009) dictyBase—a Dictyostelium bioinformatics resource update. Nucleic Acids Res 37(Database issue):D515–D519. https://doi.org/10.1093/nar/gkn844

    Article  PubMed  CAS  Google Scholar 

  25. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigo R, Hubbard TJ (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22(9):1760–1774. https://doi.org/10.1101/gr.135350.111

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40(Database issue):D700–D705. https://doi.org/10.1093/nar/gkr1029

    Article  PubMed  CAS  Google Scholar 

  27. Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M (2017) WormBase ParaSite - a comprehensive resource for helminth genomics. Mol Biochem Parasitol 215:2–10. https://doi.org/10.1016/j.molbiopara.2016.11.005

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD (2017) Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J 89(4):789–804. https://doi.org/10.1111/tpj.13415

    Article  PubMed  CAS  Google Scholar 

  29. Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LD, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol 29(10):922–927. https://doi.org/10.1038/nbt.1976

    Article  PubMed  CAS  Google Scholar 

  30. Reid I, O’Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A (2014) SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models. BMC Bioinformatics 15:229. https://doi.org/10.1186/1471-2105-15-229

    Article  PubMed  PubMed Central  Google Scholar 

  31. Testa AC, Hane JK, Ellwood SR, Oliver RP (2015) CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. BMC Genomics 16:170. https://doi.org/10.1186/s12864-015-1344-4

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M (2016) BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32(5):767–769. https://doi.org/10.1093/bioinformatics/btv661

    Article  PubMed  CAS  Google Scholar 

  33. Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G (2010) The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res 38(Database issue):D420–D427. https://doi.org/10.1093/nar/gkp751

    Article  PubMed  CAS  Google Scholar 

  34. Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2014) The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42(Database issue):D705–D710. https://doi.org/10.1093/nar/gkt1029

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ronald P. de Vries .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

de Vries, R.P., Grigoriev, I.V., Tsang, A. (2018). Introduction: Overview of Fungal Genomics. In: de Vries, R., Tsang, A., Grigoriev, I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7804-5_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7804-5_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7803-8

  • Online ISBN: 978-1-4939-7804-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics