Typically, a genome portal contains tools to
visualize and analyze the genome data. These
tools include Blast to search for homology
(Altschul et al. 1990), a search function for
functional annotations and a genome browser.
Since the generated data will likely contain
errors in gene prediction, it is important that
these predictions can be fixed manually, based
on external evidence. Genome browsers can
facilitate this in an intuitive way. Data of various origins can be displayed, evaluated, and (if
needed) manually corrected. This process is
referred to as manual curation. Data that can
be visualized include gene predictions, expression data, regions of homology (e.g., blast hits),
genome synteny, etc.
An early example of a web-based genome
browser was the UCSC (University of California, Santa Cruz) Genome Browser, which was
originally developed to visualize the human
genome (Kent et al. 2002) and is also used in
MycoCosm. Later, GBrowse was developed
(Stein 2013), which was designed to integrate
well with the Generic Model Organism Database suite (www.gmod.org). Its successor
JBrowse (Buels et al. 2016) offers an intuitive
and flexible genome browser that can be easily
installed and used in small-scale genome
sequencing initiatives. Web Apollo (later
renamed to Apollo) (Lee et al. 2013) is a plugin
for JBrowse that facilitates the manual curation
(correction) of gene predictions as well as other
genomic features, making it a valuable tool for
genome visualization, analysis, and curation.
All corrections are stored in a centralized database, allowing collaborators from all over the
world to simultaneously work on the same
genome.
IV. Genomics and Biotechnology
Fungi play important roles in a wide range of
fields that are interesting from a biotechnological perspective. Genome sequencing and annotation has greatly facilitated the development of
these fields by revealing the genes involved in
these processes. Examples of biotechnologically
relevant topics include secondary metabolites,
carbohydrate-active enzymes, mushroom
development, and plant interactions. Obviously, this is by no means an exhaustive list of
biotechnological topics. This section will discuss the roles genome sequencing and analysis
have played in these important fields of study.
A. Secondary Metabolites or Natural Products
Fungi can produce a wide range of secondary
metabolites, which are relatively small molecules that are not directly encoded by genes.
In the context of biotechnology, they are frequently referred to as natural products. These
metabolites can play an important role in processes such as pathogenesis, defense, interactions, pigmentation, etc. Often, they play an
ecological role and help the fungi to colonize a
niche. From a biotechnology perspective, they
are interesting for their antibacterial, antifungal, and antitumor activities. Some well-known
examples of natural products are the antibiotic
penicillin, which is produced by species of Penicillium (Bennett and Chung 2001), and the
cholesterol-lowering drug lovastatin (Downs
et al. 1998).
Secondary metabolites are not directly
encoded by genes, but instead they are generally
produced by a set of enzymes that synthesize
the metabolite in a conveyor belt-like fashion.
These enzymes include polyketide synthases
(PKS), non-ribosomal peptide synthetases
(NRPS), terpene cyclases (TC), dimethyl-allyltryptophan synthetases (DMATS), and a range
of accessory enzymes including methyltransferases (Keller et al. 2005; Keller 2019). Intriguingly, the genes encoding these enzymes are
frequently clustered in the genome, which
makes them relatively easy to identify (Nu ¨tzmann et al. 2018). These gene clusters are
known as biosynthetic gene clusters. AntiSMASH is a commonly used tool to identify
these clusters (Blin et al. 2017). It first identifies
core genes (PKS, NRPS, TC, and DMATS) and
then looks for putative accessory genes involved
in the production of the secondary metabolite.
Moreover, the identified putative clusters can be
compared to known clusters in other organisms. This homology and the gene families in
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R. A. Ohm
visualize and analyze the genome data. These
tools include Blast to search for homology
(Altschul et al. 1990), a search function for
functional annotations and a genome browser.
Since the generated data will likely contain
errors in gene prediction, it is important that
these predictions can be fixed manually, based
on external evidence. Genome browsers can
facilitate this in an intuitive way. Data of various origins can be displayed, evaluated, and (if
needed) manually corrected. This process is
referred to as manual curation. Data that can
be visualized include gene predictions, expression data, regions of homology (e.g., blast hits),
genome synteny, etc.
An early example of a web-based genome
browser was the UCSC (University of California, Santa Cruz) Genome Browser, which was
originally developed to visualize the human
genome (Kent et al. 2002) and is also used in
MycoCosm. Later, GBrowse was developed
(Stein 2013), which was designed to integrate
well with the Generic Model Organism Database suite (www.gmod.org). Its successor
JBrowse (Buels et al. 2016) offers an intuitive
and flexible genome browser that can be easily
installed and used in small-scale genome
sequencing initiatives. Web Apollo (later
renamed to Apollo) (Lee et al. 2013) is a plugin
for JBrowse that facilitates the manual curation
(correction) of gene predictions as well as other
genomic features, making it a valuable tool for
genome visualization, analysis, and curation.
All corrections are stored in a centralized database, allowing collaborators from all over the
world to simultaneously work on the same
genome.
IV. Genomics and Biotechnology
Fungi play important roles in a wide range of
fields that are interesting from a biotechnological perspective. Genome sequencing and annotation has greatly facilitated the development of
these fields by revealing the genes involved in
these processes. Examples of biotechnologically
relevant topics include secondary metabolites,
carbohydrate-active enzymes, mushroom
development, and plant interactions. Obviously, this is by no means an exhaustive list of
biotechnological topics. This section will discuss the roles genome sequencing and analysis
have played in these important fields of study.
A. Secondary Metabolites or Natural Products
Fungi can produce a wide range of secondary
metabolites, which are relatively small molecules that are not directly encoded by genes.
In the context of biotechnology, they are frequently referred to as natural products. These
metabolites can play an important role in processes such as pathogenesis, defense, interactions, pigmentation, etc. Often, they play an
ecological role and help the fungi to colonize a
niche. From a biotechnology perspective, they
are interesting for their antibacterial, antifungal, and antitumor activities. Some well-known
examples of natural products are the antibiotic
penicillin, which is produced by species of Penicillium (Bennett and Chung 2001), and the
cholesterol-lowering drug lovastatin (Downs
et al. 1998).
Secondary metabolites are not directly
encoded by genes, but instead they are generally
produced by a set of enzymes that synthesize
the metabolite in a conveyor belt-like fashion.
These enzymes include polyketide synthases
(PKS), non-ribosomal peptide synthetases
(NRPS), terpene cyclases (TC), dimethyl-allyltryptophan synthetases (DMATS), and a range
of accessory enzymes including methyltransferases (Keller et al. 2005; Keller 2019). Intriguingly, the genes encoding these enzymes are
frequently clustered in the genome, which
makes them relatively easy to identify (Nu ¨tzmann et al. 2018). These gene clusters are
known as biosynthetic gene clusters. AntiSMASH is a commonly used tool to identify
these clusters (Blin et al. 2017). It first identifies
core genes (PKS, NRPS, TC, and DMATS) and
then looks for putative accessory genes involved
in the production of the secondary metabolite.
Moreover, the identified putative clusters can be
compared to known clusters in other organisms. This homology and the gene families in
212
R. A. Ohm