Marine Microalgae 5.3 Microalgal Genomes 53
Part A | 5.3
ithophorids produce calcified scales called coccoliths.
Most are primarily marine species inhabiting tropical seawater. Microalgal biomass of Haptophyceae is
commonly used as living feed in aquaculture [5.17].
Isochrysis galbana and Pavlova lutheri, especially, are
used as living feed for bivalve molluscs, crustacean
larvae, and zooplanktons that in turn are used for crustacean and fish larvae. Some cells can produce PUFAs
such as docosahexaenoic acid (DHA), or EPA. In addition, the DHA content in I. galbana has been shown
to be enhanced by low temperature or incubation of
the culture in the dark after reaching the plateau phase
growth [5.18]. Furthermore, it was shown that these
algae are useful for DHA enrichment of feed such as rotifers for the larvae of several marine fish species [5.19].
In Dinophyceae, a genus Symbiodinium (dinoflagellate) has been well described. Various marine invertebrates, such as reef-building corals, jellyfish, sea
anemones, and bivalves form symbiotic associations
with Symbiodinium, commonly known as zooxanthellae. Symbiodinium strains have been classified into
more than three clades using restriction fragment length
polymorphism based on 18S rRNA sequence analysis [5.20]. The composition of Symbiodinium populations may also play an important role in the tolerance
or sensitivity of corals towards bleaching.
5.3 Microalgal Genomes
Sequencing of microbial genomes has become a routine
procedure for gene discovery and genetic engineering of microalgae. Synechocystis sp. PCC 6803 was
the first photosynthetic organism for which the entire genome sequence was determined. Currently, 72
finished cyanobacterial genome sequences are listed
in GenBank, and many additional genome analyses
are currently in progress. Most cyanobacteria possess a circular chromosome and a small number of
additional plasmids. Genome sizes range from a minimum of 1:44 Mb for the marine cyanobacterium
UCYN-A [5.21] to a maximum of 11:58 Mb for the
Calothrix sp. PCC7103 [5.22]. Prokaryotes typically
contain a single copy of their chromosome such
as Escherichia coli, while large differences between
cyanobacteria and other prokaryotes have been reported
for chromosomal copy numbers. Some cyanobacteria
are oligoploid, for example, Synechocystis sp. PCC
6803 are highly polyploid, and the motile wild-type
strain contains 218 genome copies in exponential
phase and 58 genome copies in linear and stationary
phases [5.23].
Recently, a comparative genomics-based approach
was used to screen cyanobacteria for the direct production of alkanes, the primary hydrocarbon components
of gasoline, diesel, and jet fuel [5.8]. Eleven different
cyanobacteria with available genome sequences were
grown, and their culture extracts were evaluated for hydrocarbon production. Indeed, ten of these strains produced alkanes. The comparison of predicted proteins
from these ten genomes against the eleventh finally led
to the discovery of two hypothetical proteins as candidates for alkane biosynthesis. This discovery is the
first description of genes responsible for alkane biosynthesis and the first example of a single-step conversion
of sugar to fuel-grade alkanes by an engineered microorganism. A comparison of the genome sequences
of producing and non-producing organisms led to the
identification of the responsible genes.
In eukaryotic microalgae genomics, large-scale sequencing has been demonstrated by next-generation
sequencing technologies. These have drastically increased the number of bases obtained per sequencing
run while at the same time decreasing the costs per
base. The first whole genome sequence of C. merolae
was determined in 2004 [5.26]; this was the first identiTable 5.1 Sequenced whole genomes of microalgal strains
Microalgae species
Genome length
(Mbp)
References
Ochrophyta
Phaeodactylum tricornutum
27.4
[5.24]
Thalassiosira pseudonana
32.4
[5.25]
Rhodophyta
Cyanidioschyzon merolae
16.5
[5.26]
Chlorophyta
Chlamydomonas reinhardtii 121
[5.27]
Chlorella variabilis
46.2
[5.28]
Micromonas pusilla
21.9
[5.29]
Micromonas sp.
20.9
[5.29]
Volvox carteri
138
[5.30]
Ostreococcus lucimarinus
13.2
[5.31]
Ostreococcus tauri
12.6
[5.32]
Coccomyxa subellipsoidea
48.8
[5.33]
Part A | 5.3
ithophorids produce calcified scales called coccoliths.
Most are primarily marine species inhabiting tropical seawater. Microalgal biomass of Haptophyceae is
commonly used as living feed in aquaculture [5.17].
Isochrysis galbana and Pavlova lutheri, especially, are
used as living feed for bivalve molluscs, crustacean
larvae, and zooplanktons that in turn are used for crustacean and fish larvae. Some cells can produce PUFAs
such as docosahexaenoic acid (DHA), or EPA. In addition, the DHA content in I. galbana has been shown
to be enhanced by low temperature or incubation of
the culture in the dark after reaching the plateau phase
growth [5.18]. Furthermore, it was shown that these
algae are useful for DHA enrichment of feed such as rotifers for the larvae of several marine fish species [5.19].
In Dinophyceae, a genus Symbiodinium (dinoflagellate) has been well described. Various marine invertebrates, such as reef-building corals, jellyfish, sea
anemones, and bivalves form symbiotic associations
with Symbiodinium, commonly known as zooxanthellae. Symbiodinium strains have been classified into
more than three clades using restriction fragment length
polymorphism based on 18S rRNA sequence analysis [5.20]. The composition of Symbiodinium populations may also play an important role in the tolerance
or sensitivity of corals towards bleaching.
5.3 Microalgal Genomes
Sequencing of microbial genomes has become a routine
procedure for gene discovery and genetic engineering of microalgae. Synechocystis sp. PCC 6803 was
the first photosynthetic organism for which the entire genome sequence was determined. Currently, 72
finished cyanobacterial genome sequences are listed
in GenBank, and many additional genome analyses
are currently in progress. Most cyanobacteria possess a circular chromosome and a small number of
additional plasmids. Genome sizes range from a minimum of 1:44 Mb for the marine cyanobacterium
UCYN-A [5.21] to a maximum of 11:58 Mb for the
Calothrix sp. PCC7103 [5.22]. Prokaryotes typically
contain a single copy of their chromosome such
as Escherichia coli, while large differences between
cyanobacteria and other prokaryotes have been reported
for chromosomal copy numbers. Some cyanobacteria
are oligoploid, for example, Synechocystis sp. PCC
6803 are highly polyploid, and the motile wild-type
strain contains 218 genome copies in exponential
phase and 58 genome copies in linear and stationary
phases [5.23].
Recently, a comparative genomics-based approach
was used to screen cyanobacteria for the direct production of alkanes, the primary hydrocarbon components
of gasoline, diesel, and jet fuel [5.8]. Eleven different
cyanobacteria with available genome sequences were
grown, and their culture extracts were evaluated for hydrocarbon production. Indeed, ten of these strains produced alkanes. The comparison of predicted proteins
from these ten genomes against the eleventh finally led
to the discovery of two hypothetical proteins as candidates for alkane biosynthesis. This discovery is the
first description of genes responsible for alkane biosynthesis and the first example of a single-step conversion
of sugar to fuel-grade alkanes by an engineered microorganism. A comparison of the genome sequences
of producing and non-producing organisms led to the
identification of the responsible genes.
In eukaryotic microalgae genomics, large-scale sequencing has been demonstrated by next-generation
sequencing technologies. These have drastically increased the number of bases obtained per sequencing
run while at the same time decreasing the costs per
base. The first whole genome sequence of C. merolae
was determined in 2004 [5.26]; this was the first identiTable 5.1 Sequenced whole genomes of microalgal strains
Microalgae species
Genome length
(Mbp)
References
Ochrophyta
Phaeodactylum tricornutum
27.4
[5.24]
Thalassiosira pseudonana
32.4
[5.25]
Rhodophyta
Cyanidioschyzon merolae
16.5
[5.26]
Chlorophyta
Chlamydomonas reinhardtii 121
[5.27]
Chlorella variabilis
46.2
[5.28]
Micromonas pusilla
21.9
[5.29]
Micromonas sp.
20.9
[5.29]
Volvox carteri
138
[5.30]
Ostreococcus lucimarinus
13.2
[5.31]
Ostreococcus tauri
12.6
[5.32]
Coccomyxa subellipsoidea
48.8
[5.33]