bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P2. CONSERVATION AND DIVERSITY OF SUGAR-RELATED CATABOLIC
PATHWAYS IN FUNGI
Maria Victoria Aguilar Pontes*, Eline Majoor, Claire Khosravi, Ronald P. de Vries, Miaomiao Zhou
Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology,
Utrecht University, The Netherlands.*v.aguilar@cbs.knaw.nl, e.majoor@cbs.knaw.nl, c.khosravi@cbs.knaw.nl,
r.devries@cbs.knaw.nl, m.zhou@cbs.knaw.nl
INTRODUCTION
Plant polysaccharides are among the major substrates for
many fungi. After extracellular degradation, the
monomeric components (mainly monosaccharides) are
taken up by the cells and used as carbon sources to enable
the fungus to grow. This would also imply that the range
of catabolic pathways of a fungus may be correlated to the
decomposition of the polysaccharides it can degrade.
Several carbon catabolic pathways have been studied in
different fungi able to grow on plant biomass such as
Aspergillus niger (De Vries, et al., 2012).
In this study we have tested this hypothesis by identified
the presence of genes of a number of catabolic pathways
in selected fungi from the Ascomycota and the
Basidiomycota.
METHODS
A total of 104 fungal genomes were identified from the
JGI fungal program (Grigoriev IV, et al., 2011), Broad
Institute of Harvard and MIT, AspGD (Arnaud, et al.,
2012) and NCBI genbank (Benson, et al., 2012) (data
version March 2013).
We identified A. niger genes involved in individual
pathways from literature. Genome scale protein ortholog
clusters were detected according to (Li, et al., 2003), using
inflation factor 1, E-value cutoff 1E-3, percentage match
cut off 60% as for identification of distant homologs
(Boekhorst, et al., 2007). The all-vs-all BlastP search
required by OrthoMCL was carried out in a grid of 500
computers by parallel fashion. The orthologs clusters were
then curated manually by expert knowledge and literature
search. Manual curation was aided by aligning the amino
acid sequences of the hits for each query together with a
suitable outgroup by MAFFT (Katoh, et al., 2009; Katoh,
et al., 2005), after which neighbor joining trees were
generated using MEGA5 with 1000 bootstraps. Genes that
were clearly separated from the query branch in the trees
were removed from the results.
RESULTS & DISCUSSION
Patterns of pathway gene presence are conserved among
clades. Galacturonic acid and rhamnose pathways are
missing in yeast. Pentose pathway is conserved in
Pezizomycetes and Basidiomycota, which explains their
ability to grow on pentose as carbon source (www.funggrowth.org).
These results may indicate that different evolutionary
tracks have led to different metabolic strategies.
The expression of metabolic genes will be evaluated for
those species for which transcriptome data are available.
The results will be compared to growth profiling data of
the species on a set of plant-related poly- and
monosaccharides to determine to which extent the genome
content fits the physiological ability of the species.
ACKNOWLEDGEMENTS
The comparative genomics analysis was carried out on the
Dutch national e-infrastructure with the support of SURF
Foundation (e-infra1300787).
REFERENCES
Arnaud, M.B., et al., Nucleic Acids Res, 40, 653-659 (2012).
Benson, D.A., et al., Nucleic Acids Res, 40, 48-53 (2012).
Boekhorst, J., et al., BMC Bioinformatics, 8, 356-363 (2007).
De Vries, R.P., et al. Pan Stanford Publishing Pte. Ltd, Singapore (2012).
Grigoriev IV, et al., Mycology, 2, 192-209 (2011).
Katoh, K., et al., Methods Mol Biol, 537, 39-64 (2009).
Katoh, K., et al., Nucleic Acids Res, 33, 511-518 (2005).
Li, L., et al., Genome Res, 13, 2178-2189 (2003).
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