Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

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Abstract

Background

Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/ Trichoderma.

Results

Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.

Conclusions

The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

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Most cited references 54

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Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

P. Sharp, W Li (1987)

A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

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Ab initio gene finding in Drosophila genomic DNA.

A. A. Salamov, V. V. Solovyev (2000)

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.

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Author and article information

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central

ISSN (Print): 1465-6906

ISSN (Electronic): 1465-6914

Publication date (Print): 2011

Publication date (Electronic): 18 April 2011

Publication date PMC-release: 18 April 2012

Volume: 12

Issue: 4

Page: R40

Affiliations

[1 ]Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria

[2 ]Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico

[3 ]Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA

[4 ]Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain

[5 ]División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México

[6 ]Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel

[7 ]Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India

[8 ]Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary

[9 ]DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

[10 ]School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA

[11 ]Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France

[12 ]Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia

[13 ]TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany

[14 ]Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA

[15 ]Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary

[16 ]Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain

[17 ]Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France

[18 ]Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark

[19 ]Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France

[20 ]Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy

[21 ]Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands

[22 ]Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA

Article

Publisher ID: gb-2011-12-4-r40

DOI: 10.1186/gb-2011-12-4-r40

PMC ID: 3218866

PubMed ID: 21501500

SO-VID: 54ee6c2d-3538-41c6-a5c9-22d92c8e41ae

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 31 December 2010

Date revision received : 28 March 2011

Date accepted : 18 April 2011

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Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

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Abstract

Background

Results

Conclusions

Related collections

Genome Integrity

Most cited references 54

Gene Ontology: tool for the unification of biology

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Ab initio gene finding in Drosophila genomic DNA.

Author and article information

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Comments

Comment on this article

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Cited by 239

Most referenced authors 2,661