6 Genomics of Marine Algae
195
communication between diatoms via a secreted molecule that may have important
implications for the population dynamics of algal blooms.
Phaeodactylum is also being used as an experimental system to investigate the
import of proteins into diatom plastids. As mentioned above, this is a complex process because of the four concentric membranes surrounding the plastid. Targeting of
nucleus-encoded proteins to the plastid has been shown to involve a bipartite target
sequence (Lang et al. 1998). Large-scale sequence data has allowed the comparison
of many plastid-targeted proteins leading to the identification of a conserved motif
within the bipartite target sequence (Kilian and Kroth 2005). This conserved motif
has been investigated experimentally by expressing wild type and mutant fusion
proteins in Phaeodactylum cells.
Phaeodactylum also has potential for biotechnological applications. An important advance in this area was the demonstration that transformation of this diatom
with a gene encoding a glucose transporter allowed it to grow on a carbon source
in the dark (Zaslavskaia et al. 2001). This modification allows the use of simpler
culture conditions than those necessary for light dependent growth, particularly for
large-scale cultures.
The combination of genomic data and molecular tools for post-genomic analysis of gene function is likely to provide many other insights into diatom biology
in the coming years. In parallel, additional diatom genome-sequencing projects
are underway that will provide a deeper understanding of the role of diatoms in
particular environments. Examples of the latter include projects to sequence the
genomes both of a toxic bloom diatom, Pseudo-nitzschia multieries, and of a sea
ice diatom Fragilariopsis cylindrus (Table 6.1). From a comparative point of view,
it is also important to mention that other heterokont genome sequences are available. These include two genomes from the non-photosynthetic oomycete group
(Tyler et al. 2006) and the genome of the brown macroalga Ectocarpus siliculosus (see below). The genome of another heterokont microalgae, the pelagophyte
Aureococcus anophagefferens, has also been completed recently (Table 6.1).
6.4.5.2 Prasinophyte Genomics
The prasinophytes are an ancient lineage of the Plantae and include abundant members of the marine phytoplankton. The first prasinophyte genome to be sequenced
was that of O. tauri (Derelle et al. 2006), followed rapidly by Ostreococcus
lucimarinus (Palenik et al. 2007). This genus is remarkable for several reasons;
Ostreococcus spp. are the smallest known free-living eukaryotes with a diameter
of less than 0.8 μm and each cell contains only one mitochondria and one chloroplast. Their genomes are also extremely small (12.56 Mbp for O. tauri) and highly
compact. For example, intergenic sequences in O. tauri are only 196 bp long on
average. The compaction of Ostreococcus genomes appears to have occurred under
significantly different conditions to those that have led to the extremely reduced
genomes of parasites like the microsporidian Encephalitozoon cuniculi, in as far as
the former have retained a very complete set of genes but have reduced their genome
195
communication between diatoms via a secreted molecule that may have important
implications for the population dynamics of algal blooms.
Phaeodactylum is also being used as an experimental system to investigate the
import of proteins into diatom plastids. As mentioned above, this is a complex process because of the four concentric membranes surrounding the plastid. Targeting of
nucleus-encoded proteins to the plastid has been shown to involve a bipartite target
sequence (Lang et al. 1998). Large-scale sequence data has allowed the comparison
of many plastid-targeted proteins leading to the identification of a conserved motif
within the bipartite target sequence (Kilian and Kroth 2005). This conserved motif
has been investigated experimentally by expressing wild type and mutant fusion
proteins in Phaeodactylum cells.
Phaeodactylum also has potential for biotechnological applications. An important advance in this area was the demonstration that transformation of this diatom
with a gene encoding a glucose transporter allowed it to grow on a carbon source
in the dark (Zaslavskaia et al. 2001). This modification allows the use of simpler
culture conditions than those necessary for light dependent growth, particularly for
large-scale cultures.
The combination of genomic data and molecular tools for post-genomic analysis of gene function is likely to provide many other insights into diatom biology
in the coming years. In parallel, additional diatom genome-sequencing projects
are underway that will provide a deeper understanding of the role of diatoms in
particular environments. Examples of the latter include projects to sequence the
genomes both of a toxic bloom diatom, Pseudo-nitzschia multieries, and of a sea
ice diatom Fragilariopsis cylindrus (Table 6.1). From a comparative point of view,
it is also important to mention that other heterokont genome sequences are available. These include two genomes from the non-photosynthetic oomycete group
(Tyler et al. 2006) and the genome of the brown macroalga Ectocarpus siliculosus (see below). The genome of another heterokont microalgae, the pelagophyte
Aureococcus anophagefferens, has also been completed recently (Table 6.1).
6.4.5.2 Prasinophyte Genomics
The prasinophytes are an ancient lineage of the Plantae and include abundant members of the marine phytoplankton. The first prasinophyte genome to be sequenced
was that of O. tauri (Derelle et al. 2006), followed rapidly by Ostreococcus
lucimarinus (Palenik et al. 2007). This genus is remarkable for several reasons;
Ostreococcus spp. are the smallest known free-living eukaryotes with a diameter
of less than 0.8 μm and each cell contains only one mitochondria and one chloroplast. Their genomes are also extremely small (12.56 Mbp for O. tauri) and highly
compact. For example, intergenic sequences in O. tauri are only 196 bp long on
average. The compaction of Ostreococcus genomes appears to have occurred under
significantly different conditions to those that have led to the extremely reduced
genomes of parasites like the microsporidian Encephalitozoon cuniculi, in as far as
the former have retained a very complete set of genes but have reduced their genome