9 Fungal Genomics
ROBIN A. OHM
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
II. Advances in Genome Sequencing
Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
III. Genome Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . 209
A. Repeats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
B. Gene Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
C. Functional Annotation of the Predicted
Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
D. Data Visualization, Analysis, and Manual
Curation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
IV. Genomics and Biotechnology . . . . . . . . . . . . . . . . . 212
A. Secondary Metabolites or Natural Products . . 212
B. Carbohydrate-Active Enzymes . . . . . . . . . . . . . 213
C. Mushroom Development . . . . . . . . . . . . . . . . . . . 214
D. Plant Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . 214
V. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
I. Introduction
In the past two decades, genomics has developed into a formidable tool to study various
aspects of fungi. In the year 1996, Saccharomyces cerevisiae was the first fungal genome to be
sequenced (Goffeau et al. 1996), and since then
the number of publicly available genome
sequences has increased to 2128 in GenBank
and 1398 in MycoCosm (at the time of writing
in September 2019) (Grigoriev et al. 2014; Clark
et al. 2016). Fungal genomics as a research field
was kick-started by the sequencing efforts of
institutes and consortia, including the Fungal
Genome Initiative of the BROAD Institute of
MIT and Harvard (Cuomo and Birren 2010)
and the Fungal Program of the US DOE Joint
Genome Institute (Grigoriev et al. 2011). In
recent years, sequencing costs have decreased
considerably, placing genome sequencing and
analysis well within the reach of smaller labs.
After the first fungal genome of S. cerevisiae
(Goffeau et al. 1996) was published, genome
sequencing efforts initially focused on other
previously established model systems. Examples include Neurospora crassa (Galagan et al.
2003), various species of Aspergillus (Galagan
et al. 2005), the human pathogen Cryptococcus
neoformans (Loftus et al. 2005), the plant pathogen Fusarium graminearum (Cuomo et al.
2007), and Trichoderma reesei (Martinez et al.
2008). These genome sequences are still an
indispensable tool for studying these important
model systems. Among many other things, they
facilitate high-throughput experiments such as
RNA-Seq to study genome-wide gene expression or ChIP-Seq to study various aspects of
epigenetic regulation. In combination, these
approaches aim to assign functions to regions
of the genome and are called Functional Genomics.
Moreover, the increasing number of available genome sequences (including those of
non-model organisms) allowed for a comparative genomics approach. By comparing genomes of related species, new insights can be
gained into genome evolution, gene evolution,
gene association with a particular lifestyle, as
well as phylogeny (examples of this are
described below).
In general, a genome sequencing project
starts with sequencing the genomic DNA
using next-generation sequencing technologies.
This is followed by genome assembly, which
aims to computationally reconstruct the
1 Microbiology, Department of Biology, Utrecht University,
Utrecht, the Netherlands; e-mail: r.a.ohm@uu.nl
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
ROBIN A. OHM
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
II. Advances in Genome Sequencing
Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
III. Genome Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . 209
A. Repeats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
B. Gene Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
C. Functional Annotation of the Predicted
Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
D. Data Visualization, Analysis, and Manual
Curation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
IV. Genomics and Biotechnology . . . . . . . . . . . . . . . . . 212
A. Secondary Metabolites or Natural Products . . 212
B. Carbohydrate-Active Enzymes . . . . . . . . . . . . . 213
C. Mushroom Development . . . . . . . . . . . . . . . . . . . 214
D. Plant Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . 214
V. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
I. Introduction
In the past two decades, genomics has developed into a formidable tool to study various
aspects of fungi. In the year 1996, Saccharomyces cerevisiae was the first fungal genome to be
sequenced (Goffeau et al. 1996), and since then
the number of publicly available genome
sequences has increased to 2128 in GenBank
and 1398 in MycoCosm (at the time of writing
in September 2019) (Grigoriev et al. 2014; Clark
et al. 2016). Fungal genomics as a research field
was kick-started by the sequencing efforts of
institutes and consortia, including the Fungal
Genome Initiative of the BROAD Institute of
MIT and Harvard (Cuomo and Birren 2010)
and the Fungal Program of the US DOE Joint
Genome Institute (Grigoriev et al. 2011). In
recent years, sequencing costs have decreased
considerably, placing genome sequencing and
analysis well within the reach of smaller labs.
After the first fungal genome of S. cerevisiae
(Goffeau et al. 1996) was published, genome
sequencing efforts initially focused on other
previously established model systems. Examples include Neurospora crassa (Galagan et al.
2003), various species of Aspergillus (Galagan
et al. 2005), the human pathogen Cryptococcus
neoformans (Loftus et al. 2005), the plant pathogen Fusarium graminearum (Cuomo et al.
2007), and Trichoderma reesei (Martinez et al.
2008). These genome sequences are still an
indispensable tool for studying these important
model systems. Among many other things, they
facilitate high-throughput experiments such as
RNA-Seq to study genome-wide gene expression or ChIP-Seq to study various aspects of
epigenetic regulation. In combination, these
approaches aim to assign functions to regions
of the genome and are called Functional Genomics.
Moreover, the increasing number of available genome sequences (including those of
non-model organisms) allowed for a comparative genomics approach. By comparing genomes of related species, new insights can be
gained into genome evolution, gene evolution,
gene association with a particular lifestyle, as
well as phylogeny (examples of this are
described below).
In general, a genome sequencing project
starts with sequencing the genomic DNA
using next-generation sequencing technologies.
This is followed by genome assembly, which
aims to computationally reconstruct the
1 Microbiology, Department of Biology, Utrecht University,
Utrecht, the Netherlands; e-mail: r.a.ohm@uu.nl
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020