Poster Category 1:


Phylogeny and Fungal Tree of Life



Horizontal gene transfer of katG genes from bacteroidetes into Ascomycetes

Zamocky Marcel, Furtmueller Paul, Obinger Christian

Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria


Bifunctional catalase-peroxidases (KatGs) are encoded in widely spread katG genes, useful markers for the reconstruction of the evolution of resistance against reactive oxygen species (ROS). They are present in the genomes of archaea, bacteria and fungi with bacterial KatGs being more abundant and most ancient. In fungi their physiological function still remains unclear or hypothetical. The present phylogenetic analysis reveals that katG genes were transferred from the genomes of bacteroidetes into ascomycete fungi by a single horizontal gene transfer (HGT) event. Moreover, detailed sequence analysis clearly shows the presence of two distinct groups of fungal catalase-peroxidases with katG1 genes encoding intracellular proteins (KatG1) and katG2 genes having a signal sequence thus encoding secreted peroxidases (KatG2). So far a single katG1 gene was found in the genome of the basidiomycete Ustilago mayidis, probably transferred from ascomycetes. All other known katG1 and katG2 genes are present selectively in the ascomycete genomes. Catalase-peroxidases of the first group (KatG1) are abundant mainly among Eurotiomycetes and Sordariomycetes. They are involved in removal of intracellular peroxides occurring as by-products of metabolism. On the other hand KatG2s are present in phytopathogenic fungi of the class Sordariomycetes. They may be involved in defence of phytopathogenic fungi against oxidative burst induced by the plant host after fungal invasion. Current investigation of structure-function relationship of heterologously expressed fungal katG1 & katG2 genes will shed light on their actual physiological role.



Mapping QTLs in multiple phenotypes by linkage analyses

Francisco Cubillos[2] Jonas Warringer[1] Ed Louis[2] Gianni Liti[2]

1 University of Gothenburg, 2University of Nottingham


Saccharomyces cerevisiae strains exhibit a large genotypic and phenotypic diversity, which makes this organism an attractive model for mapping quantitative trait loci (QTLs). So far only a few studies have used natural isolates to dissect complex traits and the underlying natural variation. The Saccharomyces Genome Resequencing Project (SGRP) has released genome sequence data (1 to 4X coverage) of 72 strains of S. cerevisiae and its closest known relative S. paradoxus. Half of the S. cerevisiae strains sequenced fall into five distinct clean lineages, whereas the others have mosaic recombinant genomes. Four strains representative of different clean lineages were chosen for generating a grid of six crosses. We generated 96 segregants from each cross (total of 576) and genotyped 170 loci evenly spaced along the genome (a marker every ~80 kb). Preliminary results for crossing over indicate the presence of conserved recombination hotspots between the crosses and a general reduction in recombination events in two of the crosses. All the segregants were extensively phenotyped under several conditions in order to perform linkage analysis and major QTLs were mapped for most of the phenotypes tested. Among these, high temperature growth (40ºC) and NaAsO2 (5 mM) resistance, showed the highest number of QTLs detected. For high temperature growth, several QTLs were found in specific pair combinations or shared between all crosses and little overlap was found between QTLs identified here and previously reported ones. This set of segregants will be useful to obtain a more complete picture of the genetic mechanisms underlying natural phenotypic variation.



Next-generation sequencing of the 40 Mb genome of the ascomycete Sordaria macrospora

Minou Nowrousian[2] Jason Stajich[1] Ines Engh[2] Eric Espagne[3] Jens Kamerewerd[2] Frank Kempken[4] Birgit Knab[5] Hsiao-Che Kuo[6] Heinz D. Osiewacz[5] Stefanie Pöggeler[7] Nick Read[6] Stephan Seiler[8] Kristina Smith[9] Denise Zickler[3] Michael Freitag[9] Ulrich Kück[2]

1Department of Plant Pathology and Microbiology, University of California Riverside, CA 92521, USA, 2Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany, 3Institut de Génétique et Microbiologie, Université Paris Sud UMR8621, 91405 Orsay cedex, France, 4Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany, 5Institute of Molecular Biosciences, Faculty for Biosciences and Cluster of Excellence Macromolecular Complexes, Johann Wolfgang Goethe University, 60438 Frankfurt, Germany, 6Fungal Cell Biology Group, Institute of Cell Biology, University of Edinburgh, Rutherford Building, Edinburgh, UK, 7Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany, 8Institut für Mikrobiologie und Genetik, Abteilung Molekulare Mikrobiologie, DFG Research Center Molecular Physiology of the Brain (CMPB), Universität Göttingen, Germany, 9Center for Genome Research and Biocomputing, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA


Next-generation sequencing techniques have revolutionized the way genome sequencing is done today. However, de novo assembly of eukaryotic genomes still presents significant hurdles due to their large size and stretches of repetitive sequences. Filamentous fungi usually have genomes of 30-50 Mb with few repetitive regions; therefore, their genomes are suitable candidates for de novo sequencing by next-generation sequencing techniques. Here, we present a draft version of the Sordaria macrospora genome obtained by a combination of Solexa paired-end sequencing and 454 sequencing. Paired-end Solexa sequencing of genomic DNA in libraries of 300 bp (four lanes) and 500 bp (three lanes) and an additional 10x coverage with 454 sequencing resulted in ~4 Gb of DNA sequence. The reads were assembled to a 39 Mb draft version with an N50 size of 117 kb using the Velvet assembler. By comparative analysis with the genome of Neurospora crassa, the N50 size was increased to 498 kb. Based on gene models for N. crassa, ~10000 protein coding genes were predicted. Comparison of the S. macrospora genes with that of other fungi showed that S. macrospora harbors duplications of several genes that are single-copy genes involved in self/nonself-recognition in other fungi. Furthermore, S. macrospora contains more polyketide biosynthesis genes than its close relative N. crassa, some of which might have been acquired by horizontal gene transfer. These data show that for filamentous fungi, de novo assembly of genomes from next-generation sequences alone is possible and the resulting data can be used for comparative studies to address questions of fungal biology.





Evolutionary relationships in the anthracnose pathogen Colletotrichum acutatum

Riccardo Baroncelli[1] C. Lane[1] S. Sreenivasaprasad[2]

1FERA, York, UK, 2Warick HRI, University of Warwick, UK

Colletotrichum acutatum is an important pathogen causing economically significant losses of temperate, subtropical and tropical crops. Globally, C. acutatum populations display considerable genotypic and phenotypic diversity. The overall objective is to understand the evolutionary relationships within the species with particular reference to the pathogen populations associated with the strawberry production systems in the UK.

More than 150 C. acutatum isolates related to different hosts worldwide have been assembled. Phylogenetic analysis of sequence data from the rRNA gene block-ITS region, HMG-box of the Mat1-2 gene and the beta-tubulin 2 gene led to the identification of eight distinct genetic groups within C. acutatum. The subsets of isolates represented within these genetic groups corresponded to the groups A1 - A8 identified previously based on the ITS marker. Almost all of the isolates capable of homothallic sexual reproduction, both in culture and in nature, comprise a single genetic group A7. Isolates representing populations capable of heterothallic sexual reproduction belong to two distinct genetic groups A3 and A5. Moreover, the eight genetic groups representing the global C. acutatum populations form at least two distinct clusters. Molecular characterisation of C. acutatum populations representing the introduction and spread of the pathogen in the strawberry production systems in the UK showed the presence of at least three genetic groups A2, A3 and A4. Overall, our results suggest the existence of C. acutatum populations potentially undergoing speciation processes, related to their reproductive behaviour and host association patterns.  Further molecular and phenotypic characterisation is in progress.





Analysis of regulation of pentose utilization in Aspergillus niger reveals evolutionary adaptations in the eurotiales

Evy Battaglia[1] Loek Visser[1] Anita Nijssen[1] Jerre van Veluw[1] Han A. B. Wösten[1] Ronald P. de Vries[1] [2]

1Utrecht Univeristy, 2CBS-KNAW Fungal Biodiversity Centre


D-xylose and L-arabinose are highly abundant components of plant biomass and therefore major carbon sources for many fungi. Fungi produce extracellular enzymes to release these sugars, which are subsequently taken up into the cell and converted through the pentose catabolic pathway. In Aspergilli and most other filamentous ascomycetes, D-xylose release and the pentose catabolic pathway are regulated by the transcriptional activator XlnR. In Aspergillus niger, we recently described the transcriptional activator AraR, which controls L-arabinose release and the pentose catabolic pathway. In this study we performed a phylogenetic analysis of the genes of the pentose catabolic pathway as well as the two transcriptional activators (AraR and XlnR) to identify evolutionary changes in the utilization of these sugars. This analysis showed that AraR is only present in the Eurotiales and appears to have originated from a gene duplication event (from XlnR) after this order split from the other filamentous ascomycetes. XlnR is present in all filamentous ascomycetes with the exception of members of the Onygenales. As this order is part of the same subclass, Eurothiomycetidae, as the Eurotiales, this indicates that strong adaptation of the regulation of pentose utilization has occurred at this evolutionary node.  In the Eurotiales a unique two-component regulatory system for pentose release and metabolism has been evolved, while the regulatory system has become absent in the Onygenales. In contrast, homologues for most genes of the L-arabinose/D-xylose catabolic pathway are present in all filamentous fungi, irrespective of the presence of XlnR and/or AraR, indicating that the evolutionary changes mainly affect the regulatory system and not the pathway itself.



A molecular diagnostic for tropical race 4 of the banana

M. A. Dita1,2, C. Waalwijk2, I. W. Buddenhagen3, M. T. Souza Jr2,4 and G. H. J. Kema2
1Embrapa Cassava & Tropical Fruits, Cruz das Almas, 44380-000, Bahia, Brazil;
2Plant Research International B.V., PO Box 16, 6700 AA Wageningen, the Netherlands;
31012 Plum Lane, Davis, California, USA;
4Embrapa LABEX Europe, PO Box 16, 6700 AA, Wageningen, the Netherlands


This study analysed genomic variation of the translation elongation factor 1α (TEF-1) and the intergenic spacer region (IGS) of the nuclear ribosomal operon of Fusarium oxysporum f. sp. cubense (Foc) isolates, from different banana production areas, representing strains within the known races, comprising 20 vegetative compatibility groups (VCG). Based on two single nucleotide polymorphisms present in the IGS region, a PCR-based diagnostic tool was developed to specifically detect isolates from VCG 01213, also called tropical race 4 (TR4), which is currently a major concern in global banana production. Validation involved TR4 isolates, as well as Foc isolates from 19 other VCGs, other fungal plant pathogens and DNA samples from infected tissues of the Cavendish banana cultivar Grand Naine (AAA). Subsequently, a multiplex PCR was developed for fungal or plant samples that also discriminated Musa acuminata and M. balbisiana genotypes. It was concluded that this diagnostic procedure is currently the best option for the rapid and reliable detection and monitoring of TR4 to support eradication and quarantine strategies.





Development of the Aspergillus oryzae comparative fungal genome database

Kazuhiro Iwashita, Kazutoshi Sakamoto, Osamu Yamada

National research institute of brewing, Japan


By the recent advancement of genome sequencing technology, the numerous numbers of genome sequences have been reported in several industrial and pathogenic fungi.  The comparative genomic of these fungi will supply us huge noble information for phylogenetic study, identification of specie specific genes cluster, identification of genes function and etc.  Several genome database was established including Aspergillus species and published.  The genome sequence of Aspergillus oryzae was also deposited and published in these databases.  However, available information is not sufficient in the point of comparative genomics, especially, comparison of well studied genome, such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Aspergillus nidulans.  Thus, we developed Aspergillus oryzae comparative fungal genome database (NRIB CFGD) in this study. First of all, we enriched the CDS information of A. oryzae genes, such as the result of motif and domain analysis, blast analysis against KOG, COG, and Swissprot, assign of EC number and expression profile of this fungi.  Furthermore, we compared the A. oryzae genome against 13 other fungal genomes.  Among them, authologous genes were clustered by bidirectional best-hit analysis.  These information were supplied with graphical interface and user can browse locus, transcripts, CDS, expression profiles, and result of authologous gene analysis very easily.  In the comparative genome site, user can browse dot blot analysis, differential analysis and the comparison of synteny of genes. This database will be opened soon and waiting for your access.





Variation in sequence and location of the fumonisin mycotoxin biosynthetic gene cluster in Fusarium

Robert Proctor[3]  François Van Hove[1] Antonia Susca[2] Gaetano Stea[2] Mark Busman[3] Theo van der Lee[4] Cees Waalwijk[4] Antonio Moretti[2]

1Mycothèque de l’Université catholique de Louvain (MUCL), Louvain-la-Neuve, Belgium, 2National Research Council, ISPA, Bari, Italy, 3US Department of Agriculture, ARS, NCAUR, Peoria, Illinois, USA, 4Plant Research International B.V., Wageningen, The Netherlands


Several Fusarium species in the Gibberella fujikuroi species complex (GFSC) and rare strains of F. oxysporum can produce fumonisins, a family of mycotoxins associated with multiple health disorders in humans and animals.  In Fusarium, the ability to produce fumonisins is governed by a 17-gene fumonisin biosynthetic gene (FUM) cluster.  Here, we examined the cluster in F. oxysporum strain O-1890 and nine other species (e.g. F. proliferatum and F. verticillioides) selected to represent a wide range of the genetic diversity within the GFSC.  Flanking-gene analysis revealed that the FUM cluster can be located in one of four genetic environments.  Comparison of the genetic environments with a housekeeping gene-based species phylogeny revealed that FUM cluster location is correlated with the phylogenetic relationships of species; the cluster is in the same genetic environment in more closely related species and different environments in more distantly related species.  Additional analyses revealed that sequence polymorphism in the FUM cluster is not correlated with phylogenetic relationships among some species.  However, cluster polymorphism is associated with production of different classes of fumonisins in some species.  As a result, closely related species can have markedly different FUM gene sequences and can produce different classes of fumonisins.  The data indicate that the FUM cluster has moved within the Fusarium genome during evolution of the GFSC and further that sequence polymorphism was sometimes maintained during the movement such that clusters with markedly different sequences are now located in the same genetic environment.





Relationships among Lasiodiplodia theobromae isolates associated with tropical fruit plants inferred from the analysis of ITS and EF1-α gene

Celli Rodrigues Muniz[1] Gilvan Ferreira da Silva[1] F.C.O. Freire[1] M.I.F Guedes[2] Manoel Teixeira Souza Júnior[1] Gert Kema[3] Henk Jalink[3]

1Embrapa, 2 UECE, 3Wageningen University


Lasiodiplodia theobromae is a phytopathogenic fungus causing gummosis, a threatening disease for cashew plants in Brazil. A collection of isolates of L. theobromae obtained from cashew plants and also from others tropical fruit plants was studied on the basis of sequence data from the ITS regions and EF1-α gene. Sequence data and ITS-RFLP patterns indicate a substantial genetic variability among isolates from cashew plants showing symptoms of the disease and also from others tropical fruit plants, such as lemon, Spondia sp., passion fruit and graviola plants. However, no difference was found among L. theobromae isolates from symptomatic cashew plants and from symptomless cashew plants colonized by the fungus, indicating that possibly the same specie that endophytically colonize the cashew plants with no apparent symptoms is also responsible for the disease.   Further studies based on detection of Single Nucleotide Polymorphisms are being carried out and have   potential utility for detection of L. theobromae strains in cashew plant seedlings.   





The draft genome sequence of Mycosphaerella fijiensis, the black sigatoka pathogen of banana  

GHJ Kema1, SB Goodwin2, TAJ van der Lee1, B Dhillon2, R Arango1, CF Crane2, 1C Diaz, 3M Souza, 4J Carlier, 5J Schmutz, 6IV Grigoriev

1Plant Research International, Wageningen UR, PO box 69, 6700AB Wageningen 2USDA-ARS, 915 West State Street, Purdue University, West Lafayette, IN, USA 3Embrapa LABEX Europe, PO box 16, 6700 AA Wageningen, The Netherlands 4CIRAD, UMR 385, Campus de Baillarguet, 34398 Montpellier 5HudsonAlpha Institute, 601 Genome Way, Huntsville, AL 35806-2908, USA 6DOE-JGI, Production Genomics Facility, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA


Mycosphaerella fijiensis (anamorph: Paracercospora fijiensis) is a hemibiotrophic fungal pathogen of banana and the causal agent of the devastating Black Sigatoka or black leaf streak disease. Its control requires weekly fungicide applications when bananas are grown under disease-conducive conditions, which mostly represent precarious tropical environments. We started a multidisciplinary research program on M. fijiensis that is aiming at pesticide reduction. The first goal was to collect genomic data and to develop tools for molecular analysis of this pathosystem. Analyses of electrophoretic karyotypes on DNA extracted from protoplasts of M. fijiensis showed that chromosome sizes range between 500 kb and ~12 Mb. An extraordinarily high level of chromosome length polymorphism is observed among the M. fijiensis strains coming from both different global populations as well as within a single field population. The results suggest that sexual recombination and chromosome size polymorphisms are important in the evolution of M. fijiensis. A genetic linkage map comprising 19 linkage groups covering 1417 cM containing 235 Diversity Array Technology markers, 87 microsatellite (SSR) and three minisatellite (VNTR) markers was calculated using high LOD scores (LOD >10). All markers were sequenced and aligned to the draft 7.8x whole genome shotgun Sanger sequence of M. fijiensis CIRAD86. In addition more than 30,000 ESTs from three in vitro libraries were sequenced. The latest whole genome assembly of the shotgun reads was constructed with the JGI Arachne assembler and coordinated with the aforementioned genetic linkage map. The genome has an estimated size of 74 Mb and is now assembled into 56 scaffolds covering more than 99% of the genome. The largest scaffold is 11.8 Mb in length and 28 scaffolds (99.8. %) are larger than 50 Kb. The genome size of M. fijiensis is 80% larger than that of M. graminicola mostly due to the presence of additional repeated sequences. The current draft release, version 1.0, includes a total of 10,327 gene models predicted and functionally annotated using the JGI annotation pipeline. The availability of the M. fijiensis genome will greatly assist future studies aimed at the control of black leaf streak disease as well as genomic comparisons with many other agronomically important Dothideomycetes fungi that currently are being sequenced through the Fungal Genome Program at the U.S. Department of Energy’s Joint Genome Institute.





CADRE: An update on web services and data

Jane Mabey Gilsenan,  Paul Bowyer, David Denning

University of Manchester, Manchester, UK


The Central Aspergillus Data Repository (CADRE; is a public resource for viewing assemblies and annotated genes arising from various world-wide Aspergillus projects. We currently house data for nine genomes, including the most recent annotation contributed by the Eurofungbase Aspergillus nidulans project. We have continued to manually annotate this genome and have shared it with other relevant resources such as AspGD ( and Ensembl Genomes  ( These collaborations have helped to further improve gene structures and naming within A. nidulans annotation and, more importantly, to provide consistency across resources.

Ensembl Genomes is a new resource that seeks to complement the current Ensembl collection (predominantly vertebrate) by including other taxonomic groups. With limited expertise, this can only be done with the support of specific research communities. Therefore, as representative data of the Aspergillus community, CADRE has been integrated into Ensembl Genomes and is maintained by both teams. This collaboration has allowed us to further embellish annotation and to perform comparative analyses across eight of the genomes. Towards the end of this integration project, we were also able to submit the A. nidulans Eurofungbase annotation to EMBL with post-project contributions from CADRE, AspGD and Ensembl Genomes.





Genetic biodiversity of Trichoderma from Poland

Lidia Błaszczyk[1] Delfina Popiel[1] Jerzy Chełkowski[1] Grzegorz Koczyk[1] Agnieszka Gąbka[1] Gary J.Samuels[2]

1Institute of Plant Genetics, Polish Academy of Sciences, Poland, 2United States Dept. of Agriculture, Agriculture Research Service, Systematic Mycology and Microbiology Lab. , Rm. 304, B-011A, 10300 Baltimore Ave. Beltsville, MD 20705 U.S.A


Towards assessing the occurrence and genetic diversity of Trichoderma, we have used 222 isolates originated from different region and ecological niches of Poland. Isolates were identified at the species level by sequence analysis of their internal transcribed spacer ITS1 -  ITS2 of the rDNA cluster, the four and five intron of translation elongation factor 1- alpha (tef1) (using program TrichOKEY v 2 and TrichoBLAST identification tools) and phylogenetic analysis. Fifty three strains were positively identified as Trichoderma viride, fifty two as T. harzianum, twenty five as T. koningii, eighteen as T. citrinoviride, sixteen as T. atroviride, fifteen as T. viridescens, thirteen as T. hamatum, eight as T. virens, five as T. aggressivum, four as T. asperellum,  three as T. longibrachiatum, three as T. longipile, two as T. koningiopsis and single strains of T. cremum, T. gamsii, T. tomentosum, H. hunua, H. parapilulifera.

Finally, we identified 18 species among 222 isolates. These data suggest a relatively low genetic diversity of Trichoderma species in Poland.




The KP4 gene family

Daren W. Brown

Bacterial Foodborne Pathogens and Mycology Research, USDA-ARS-NCAUR, Peoria, IL  61604, USA



Microbial communities can play a critical role in agricultural ecosystems.  In fungal-fungal interactions, an organism can produce metabolites that elicit a physiological response in other organisms that can affect the outcome of the interaction.  Understanding this communication process maybe critical to maximize crop disease control and therefore crop production.  Small, cysteine-rich proteins, synthesized by plants, fungi, viruses and bacteria, can serve as antimicrobial peptides and can be an integral part of their defense system.  KP4, produced by the Ustilago maydis P4 virus, is one of these proteins and inhibits growth of other fungi, including Fusarium and Aspergillus, by blocking calcium ion channels.  The mature KP4 protein is 105 amino acids and contains 10 cysteine residues.  Here, analysis of publicly available genomic sequence databases identified 36 KP4-like genes from a range of Ascomycota, a Basidiomycota, and the moss Physcomitrella patens.  Six of the KP4-like genes encode a protein with two KP4 domains.  Sequence comparison and phylogenetic analysis of the corresponding proteins/domains has provided insight in to the evolutionary history of the KP4 family and provided evidence for lateral gene transfer between kingdoms.  The data also suggest that duplication to form a KP4 dimer occurred independently in different lineages of the Ascomycota.  Understanding the nature and function of KP4 proteins in mycotoxin-producing species of Fusarium may help to limit plant diseases and increase food safety and food production.



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