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S.M. Coelho et al.
with a possible role in the formation of these cell walls. This approach involves the
construction of a microarray bearing oligonucleotides corresponding to contiguous
sequences along the length of each chromosome so that transcription of any part of
the genome can be detected by hybridising with labelled cDNA. The Thalassiosira
tiling array oligonucleotides corresponded to 36 nucleotide-long regions separated
by 10 base pair gaps (Mock et al. 2008). This experiment identified a set of 75
genes that were induced under conditions of limiting silica. Another set of genes
was induced when both silica and iron were limiting, showing possible interactions
between these two metabolisms or, alternatively, that iron is a required cofactor
for silica metabolism. Interestingly, these experiments also identified 3,000 new
genes, which had not been annotated previously, including non-coding and antisense
RNAs.
Diatoms fall into two major morphological groups, centric and pennate
(Thalassiosira being a centric diatom), and recently a second genome sequence has
been completed for the pennate diatom, P. tricornutum (Bowler et al. 2008). One of
the most striking outcomes of the analysis of this second diatom genome was the
identification of hundreds of genes that appear to have been acquired from bacteria
by horizontal gene transfer. These genes represent at least 5% of the genome, suggesting that the extent of horizontal gene transfer has been an order of magnitude
higher in the diatoms than in other free-living eukaryotes that were the subject of
previous studies.
The availability of genome data for two diatom species has permitted comparative analyses of several aspects of diatom metabolism including nitrogen and
carbon metabolism and carotenoid biosynthesis (Allen et al. 2006, Coesel et al.
2008, Kroth et al. 2008). Several observations suggest that the growth of diatoms
in their marine environments is not limited by the available CO 2 . The genomes of
both T. pseudonana and P. tricornutum potentially encode all of the enzymes necessary for C 4 -photosynthesis (Kroth et al. 2008) raising the intriguing possibility that,
despite its high energetic cost, C 4 -photosynthesis could give a critical ecological
advantage in CO 2 -limiting conditions, such as in phytoplankton blooms. Moreover,
recent experimental work indicates that a wide range of diatoms may use C 4 -based
CO 2 -concentrating mechanisms (McGinn and Morel 2008).
One strong argument for sequencing the Phaeodactylum genome was the
amenability of this organism to laboratory experimentation. It can be transformed
(Zaslavskaia et al. 2000) and a number of molecular tools have been developed to
analyse gene expression and gene function (Siaut et al. 2007). A recent study of
aldehyde-based cell-to-cell signalling illustrates how such experimental approaches
can provide insights into processes that may play key roles in diatom ecology in
the oceans. Diatoms are known to produce reactive aldehydes as defence molecules
(Ianora et al. 2004). Addition of the aldehyde (2E,4E/Z)-decadienal (DD) to laboratory cultures of Phaeodactylum induced intracellular calcium transients and the
generation of nitric oxide (NO), inducing cell death. Diatoms treated with a low
concentration of the aldehyde, however, developed a resistance to the toxic effects
of the higher dose. These observations indicate the existence of a system that allows
S.M. Coelho et al.
with a possible role in the formation of these cell walls. This approach involves the
construction of a microarray bearing oligonucleotides corresponding to contiguous
sequences along the length of each chromosome so that transcription of any part of
the genome can be detected by hybridising with labelled cDNA. The Thalassiosira
tiling array oligonucleotides corresponded to 36 nucleotide-long regions separated
by 10 base pair gaps (Mock et al. 2008). This experiment identified a set of 75
genes that were induced under conditions of limiting silica. Another set of genes
was induced when both silica and iron were limiting, showing possible interactions
between these two metabolisms or, alternatively, that iron is a required cofactor
for silica metabolism. Interestingly, these experiments also identified 3,000 new
genes, which had not been annotated previously, including non-coding and antisense
RNAs.
Diatoms fall into two major morphological groups, centric and pennate
(Thalassiosira being a centric diatom), and recently a second genome sequence has
been completed for the pennate diatom, P. tricornutum (Bowler et al. 2008). One of
the most striking outcomes of the analysis of this second diatom genome was the
identification of hundreds of genes that appear to have been acquired from bacteria
by horizontal gene transfer. These genes represent at least 5% of the genome, suggesting that the extent of horizontal gene transfer has been an order of magnitude
higher in the diatoms than in other free-living eukaryotes that were the subject of
previous studies.
The availability of genome data for two diatom species has permitted comparative analyses of several aspects of diatom metabolism including nitrogen and
carbon metabolism and carotenoid biosynthesis (Allen et al. 2006, Coesel et al.
2008, Kroth et al. 2008). Several observations suggest that the growth of diatoms
in their marine environments is not limited by the available CO 2 . The genomes of
both T. pseudonana and P. tricornutum potentially encode all of the enzymes necessary for C 4 -photosynthesis (Kroth et al. 2008) raising the intriguing possibility that,
despite its high energetic cost, C 4 -photosynthesis could give a critical ecological
advantage in CO 2 -limiting conditions, such as in phytoplankton blooms. Moreover,
recent experimental work indicates that a wide range of diatoms may use C 4 -based
CO 2 -concentrating mechanisms (McGinn and Morel 2008).
One strong argument for sequencing the Phaeodactylum genome was the
amenability of this organism to laboratory experimentation. It can be transformed
(Zaslavskaia et al. 2000) and a number of molecular tools have been developed to
analyse gene expression and gene function (Siaut et al. 2007). A recent study of
aldehyde-based cell-to-cell signalling illustrates how such experimental approaches
can provide insights into processes that may play key roles in diatom ecology in
the oceans. Diatoms are known to produce reactive aldehydes as defence molecules
(Ianora et al. 2004). Addition of the aldehyde (2E,4E/Z)-decadienal (DD) to laboratory cultures of Phaeodactylum induced intracellular calcium transients and the
generation of nitric oxide (NO), inducing cell death. Diatoms treated with a low
concentration of the aldehyde, however, developed a resistance to the toxic effects
of the higher dose. These observations indicate the existence of a system that allows