Abstract
The functional genomics project “TrichoEST” was developed focused on different taxonomic groups of Trichoderma with biocontrol potential. Four cDNA libraries were constructed, using similar growth conditions, from four different Trichoderma strains: Trichoderma longibrachiatum T52, Trichoderma asperellum T53, Trichoderma virens T59, and Trichoderma sp. T78. In this study, we present the analysis of the 8,160 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1,000–1,300 unique sequences were identified in each strain. First, we queried our collection of ESTs against the NCBI nonredundant database using the BLASTX algorithm. Moreover, using the Gene Ontology hierarchy, we performed the annotation of 40.9% of the unique sequences. Later, based on the EST abundance, we examined the highly expressed genes in the four strains. A hydrophobin was found as the gene expressed at the highest level in two of the strains, but we also found that other unique sequences similar to the HEX1, QID3, and NMT1 proteins were highly represented in at least two of the Trichoderma strains.
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Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Arvas M, Pakula T, Lanthaler K, Saloheimo M, Valkonen M, Suortti T, Robson G, Penttila M (2006) Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics 7:32
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Askolin S, Penttila M, Wosten HA, Nakari-Setala T (2005) The Trichoderma reesei hydrophobin genes hfb1 and hfb2 have diverse functions in fungal development. FEMS Microbiol Lett 253:281–288
Austin R, Provart NJ, Sacadura NT, Nugent KG, Babu M, Saville BJ (2004) A comparative genomic analysis of ESTs from Ustilago maydis. Funct Integr Genomics 4:207–218
Bell-Pedersen D, Shinohara ML, Loros JJ, Dunlap JC (1996) Circadian clock-controlled genes isolated from Neurospora crassa are late night- to early morning-specific. Proc Natl Acad Sci USA 93:13096–13101
Benítez T, Rincón AM, Limón MC, Codón AC (2004) Biocontrol mechanisms of Trichoderma strains. Int Microbiol 7:249–260
Carpenter MA, Stewart A, Ridgway HJ (2005) Identification of novel Trichoderma hamatum genes expressed during mycoparasitism using subtractive hybridisation. FEMS Microbiol Lett 251:105–112
Chambergo FS, Bonaccorsi ED, Ferreira AJ, Ramos AS, Ferreira JRJJR, Abrahao-Neto J, Farah JP, El-Dorry H (2002) Elucidation of the metabolic fate of glucose in the filamentous fungus Trichoderma reesei using expressed sequence tag (EST) analysis and cDNA microarrays. J Biol Chem 277:13983–13988
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Curach NC, Te’o VS, Gibbs MD, Bergquist PL, Nevalainen KM (2004) Isolation, characterization and expression of the hex1 gene from Trichoderma reesei. Gene 331:133–140
Diener SE, Dunn-Coleman N, Foreman P, Houfek TD, Teunissen PJ, van Solingen P, Dankmeyer L, Mitchell TK, Ward M, Dean RA (2004) Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei. FEMS Microbiol Lett 230:275–282
Ebbole DJ, Jin Y, Thon M, Pan H, Bhattarai E, Thomas T, Dean R (2004) Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags. Mol Plant-Microb Interact 17:1337–1347
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
Foreman PK, Brown D, Dankmeyer L, Dean R, Diener S, Dunn-Coleman NS, Goedegebuur F, Houfek TD, England GJ, Kelley AS, Meerman HJ, Mitchell T, Mitchinson C, Olivares HA, Teunissen PJ, Yao J, Ward M (2003) Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei. J Biol Chem 278:31988–31997
Freimoser FM, Screen S, Hu G, St Leger R (2003) EST analysis of genes expressed by the zygomycete pathogen Conidiobolus coronatus during growth on insect cuticle. Microbiology 149:1893–1900
Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly WW, Gathman AC (2003) ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media. Fungal Genet Biol 39:191–198
Hermosa MR, Keck E, Chamorro I, Rubio B, Sanz L, Vizcaino JA, Grondona I, Monte E (2004) Genetic diversity shown in Trichoderma biocontrol isolates. Mycol Res 108:897–906
Howell CR (2003) Mechanisms employed by Trichoderma species in the biological control of plant diseases: the history and evolution of current concepts. Plant Dis 87:4–10
Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877
Keon J, Antoniw J, Rudd J, Skinner W, Hargreaves J, Hammond-Kosack K (2005) Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici). Fungal Genet Biol 42:376–389
Kim S, Ahn IP, Lee YH (2001) Analysis of genes expressed during rice-Magnaporthe grisea interactions. Mol Plant Microb Interact 14:1340–1346
Kurtov D, Kinghorn JR, Unkles SE (1999) The Aspergillus nidulans panB gene encodes ketopantoate hydroxymethyltransferase, required for biosynthesis of pantothenate and Coenzyme A. Mol Gen Genet 262:115–120
Liu PG, Yang Q (2005) Identification of genes with a biocontrol function in Trichoderma harzianum mycelium using the expressed sequence tag approach. Res Microbiol 156:416–423
Lora JM, de la Cruz J, Benitez T, Llobell A, Pintor-Toro JA (1994) A putative catabolite-repressed cell wall protein from the mycoparasitic fungus Trichoderma harzianum. Mol Gen Genet 242:461–466
Lora JM, Pintor-Toro JA, Benitez T, Romero LC (1995) Qid3 protein links plant bimodular proteins with fungal hydrophobins. Mol Microbiol 18:380–382
Markham P, Collinge AJ (1987) Woronin bodies of filamentous fungi. FEMS Microbiol Rev 46:1–11
Monte E (2001) Understanding Trichoderma: between biotechnology and microbial ecology. Int Microbiol 4:1–4
Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P (2003) Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 21:790–795
Nugent KG, Choffe K, Saville BJ (2004) Gene expression during Ustilago maydis diploid filamentous growth: EST library creation and analyses. Fungal Genet Biol 41:349–360
Penttila M, Nevalainen H, Ratto M, Salminen E, Knowles J (1987) A versatile transformation system for the cellulolytic filamentous fungus Trichoderma reesei. Gene 61:155–164
Posada-Buitrago ML, Frederick RD (2005) Expressed sequence tag analysis of the soybean rust pathogen Phakopsora pachyrhizi. Fungal Genet Biol 42:949–962
Rey M, Llobell A, Monte E, Scala F, Lorito M (2004) Genomics of Trichoderma. In: Khachatourians GG (ed) Fungal genomics. Elsevier Science, Amsterdam
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277
Sanz L, Montero M, Grondona I, Vizcaíno JA, Llobell A, Hermosa R, Monte E (2004) Cell wall-degrading isoenzyme profiles of Trichoderma biocontrol strains show correlation with rDNA taxonomic species. Curr Genet 46:277–286
Semova N, Storms R, John T, Gaudet P, Ulycznyj P, Min XJ, Sun J, Butler G, Tsang A (2006) Generation, annotation, and analysis of an extensive Aspergillus niger EST collection. BMC Microbiol 6:7
Sivasithamparam K, Ghisalberti EL (1998) Secondary metabolism in Trichoderma and Gliocladium. In: Harman GE, Kubicek CP (eds) Trichoderma and Gliocladium, vol. 1. Taylor & Francis, London, UK, pp 139–191
Soundararajan S, Jedd G, Li X, Ramos-Pamplona M, Chua NH, Naqvi NI (2004) Woronin body function in Magnaporthe grisea is essential for efficient pathogenesis and for survival during nitrogen starvation stress. Plant Cell 16:1564–1574
St Leger RJ, Frank DC, Roberts DW, Staples RC (1992a) Molecular cloning and regulatory analysis of the cuticle-degrading-protease structural gene from the entomopathogenic fungus Metarhizium anisopliae. Eur J Biochem 204:991–1001
St Leger RJ, Staples RC, Roberts DW (1992b) Cloning and regulatory analysis of starvation-stress gene, ssgA, encoding a hydrophobin-like protein from the entomopathogenic fungus, Metarhizium anisopliae. Gene 120:119–124
St Leger R, Joshi L, Bidochka MJ, Roberts DW (1996) Construction of an improved mycoinsecticide overexpressing a toxic protease. Proc Natl Acad Sci USA 93:6349–6354
Viaud MC, Balhadere PV, Talbot NJ (2002) A Magnaporthe grisea cyclophilin acts as a virulence determinant during plant infection. Plant Cell 14:917–930
Viterbo A, Ramot O, Chemin L, Chet I (2002) Significance of lytic enzymes from Trichoderma spp. in the biocontrol of fungal plant pathogens. Antonie Van Leeuwenhoek 81:549–556
Vizcaíno JA, Sanz L, Basilio A, Vicente F, Gutiérrez S, Hermosa MR, Monte E (2005) Screening of antimicrobial activities in Trichoderma isolates representing three trichoderma sections. Mycol Res 109:1397–1406
Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M (2006) Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics 7:193
Wang P, Heitman J (2005) The cyclophilins. Genome Biol 6:226
Acknowledgements
First, the authors want to acknowledge the financial support of the European Commission to the project “TrichoEST” (QLK3-CT-2002-02032) and the “Fundación Ramón Areces”. We want to recognize the work carried out by I. Chamorro, E. Keck, J.A. de Cote, I. González, and M. Andrada for their technical support. Authors want also to acknowledge R. Jiménez, A. Gaignard, M. P. García-Pastor, and J. Heinrich, who helped in different bioinformatics related tasks. Additionally, we want to thank C. Mungall for his help in setting up the AmiGO browser. This manuscript is dedicated to Prof. Antonio Llobell because without his contribution, this project could not be carried out.
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Vizcaíno, J.A., Redondo, J., Suárez, M.B. et al. Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol. Appl Microbiol Biotechnol 75, 853–862 (2007). https://doi.org/10.1007/s00253-007-0885-0
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DOI: https://doi.org/10.1007/s00253-007-0885-0