Poster Category
1:
Phylogeny and Fungal Tree of Life
PR1.1
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
marcel.zamocky@boku.ac.at
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.
PR1.2
Francisco Cubillos[2]
Jonas Warringer[1] Ed Louis[2] Gianni Liti[2]
1
University of Gothenburg, 2University of
plxfc@exmail.nottingham.ac.uk
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.
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.
Riccardo Baroncelli[1]
C. Lane[1] S. Sreenivasaprasad[2]
1FERA,
R.Baroncelli@warwick.ac.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
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
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
e.battaglia@uu.nl
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
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
cees.waalwijk@wur.nl
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.
Kazuhiro Iwashita,
Kazutoshi Sakamoto, Osamu Yamada
National research institute of brewing,
iwashitact@nrib.go.jp
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
robert.proctor@ars.usda.gov
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.
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
celli@cnpat.embrapa.br
Lasiodiplodia theobromae
is a phytopathogenic fungus causing gummosis, a threatening disease for cashew
plants in
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
rt.kema@wur.nl
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.
Jane Mabey Gilsenan,
Paul Bowyer, David Denning
e.gilsenan@manchester.ac.uk
The Central
Aspergillus Data Repository (CADRE;
http://www.cadre-genomes.org.uk) 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
(http://www.aspergillusgenome.org) and Ensembl Genomes
(http://www.ensemblgenomes.org). 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.
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
dpop@igr.poznan.pl
Towards assessing the occurrence and genetic diversity of
Trichoderma, we have used 222 isolates originated from different
region and ecological niches of
Finally, we identified 18 species among 222 isolates. These data suggest a
relatively low genetic diversity of
Trichoderma species in
The KP4 gene family
Daren W. Brown
Bacterial Foodborne Pathogens and Mycology Research, USDA-ARS-NCAUR,
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.