202
S.M. Coelho et al.
2003). The species harvested are principally from the genera Porphyra, for consumption as nori, and Eucheuma and Kappaphycus, for carrageenan production. The
red algae are an ancient eukaryotic group; estimated to have originated about 1,500
Mya (Yoon et al. 2004). Fossils of red algae exhibiting evidence of multicellular
development and sexuality have been dated at approximately 1,200 Mya, indicating
that this group was the first to evolve complex multicellularity (Butterfield 2000).
As with the brown algae, this ancient evolutionary history is correlated with many
unusual features such as their complex life cycles and novel metabolic processes;
the latter particularly in terms of the production of oxilipins, cell polysaccharides
and halogenated compounds (Siegel and Siegel 1973, Manley 2002, Bouarab et al.
1999, Coelho et al. 2007). As discussed above, red algae also played a key role in
the evolutionary history of photosynthesis, notably via the endosymbiotic processes
that led to the evolution of secondary chloroplasts.
Taken together these features provide strong arguments for using genomic
approaches to explore red algal genomes. EST sequences are available for several species of red macroalga, including Porphyra yezoensis (20,000 ESTs, Nikaido
et al. 2000, Asamizu et al. 2003), Chondrus crispus (4,056 ESTs, Collén et al.
2006b), Gracilaria tenuistipitata (3,000 ESTs, Pi Nyvall, personnal communication) and Griffithsia okiensis (1,104 ESTs, Lee et al. 2007), and cDNA micro- or
macroarrays have been used to monitor gene expression in both Chondrus crispus (Collén et al. 2006a) and Porphyra yezoensis (Kitade et al. 2008). However,
currently the only complete red algal genome sequence available is that of
C. merolae, a unicellular organism from hot acid springs that has a highly reduced
and unusual genome. A second project is in progress, for Galdieria sulphuraria,
(http://genomics.msu.edu/galdieria/about.html) but this is also a non-marine, unicellular, extremophile red alga. Both of these organisms have very small, highly
derived genomes, which are of limited relevance to understanding many red algal
features. A genome sequence for a more “typical” red alga would be extremely
useful both to further our understanding of red algal biology and as a reference
for tracing the origins of genes acquired via endosymbiotic events. In response to
this need, genome projects have recently been initiated for two red macroalgae,
the florideophyte Chondrus crispus (at Genoscope, France) and the bangiophyte
Porphyra umbilicalis (at the Joint Genome Institute, USA).
These two genome projects are likely to be highly compatible. Both seaweeds
are ecologically important in specific habitats. They can both be handled relatively
easily in the laboratory and each has been the subject of extensive laboratory studies. Porphyra spp. are perhaps the best adapted to laboratory work, previous studies
have reported the isolation of mutant strains (Ohme and Miura 1988, Mitman and
van der Meer 1994, Yan et al. 2000), identification of genetic markers (Park et al.
2007), the preparation and regeneration of protoplasts (Waaland et al. 1990), whole
mount in situ hybridisation (Shimizu et al. 2004) and progress towards the development of genetic transformation (Cheney et al. 2001, He et al. 2001, Lin et al.
2001). Indeed, a related species, Porphyra yezoensis, has been proposed as a candidate model macroalgae (Kitade et al. 2004, Waaland et al. 2004). C. crispus has
the advantage of possessing a smaller genome (150 Mbp, Peters et al. 2004) than
S.M. Coelho et al.
2003). The species harvested are principally from the genera Porphyra, for consumption as nori, and Eucheuma and Kappaphycus, for carrageenan production. The
red algae are an ancient eukaryotic group; estimated to have originated about 1,500
Mya (Yoon et al. 2004). Fossils of red algae exhibiting evidence of multicellular
development and sexuality have been dated at approximately 1,200 Mya, indicating
that this group was the first to evolve complex multicellularity (Butterfield 2000).
As with the brown algae, this ancient evolutionary history is correlated with many
unusual features such as their complex life cycles and novel metabolic processes;
the latter particularly in terms of the production of oxilipins, cell polysaccharides
and halogenated compounds (Siegel and Siegel 1973, Manley 2002, Bouarab et al.
1999, Coelho et al. 2007). As discussed above, red algae also played a key role in
the evolutionary history of photosynthesis, notably via the endosymbiotic processes
that led to the evolution of secondary chloroplasts.
Taken together these features provide strong arguments for using genomic
approaches to explore red algal genomes. EST sequences are available for several species of red macroalga, including Porphyra yezoensis (20,000 ESTs, Nikaido
et al. 2000, Asamizu et al. 2003), Chondrus crispus (4,056 ESTs, Collén et al.
2006b), Gracilaria tenuistipitata (3,000 ESTs, Pi Nyvall, personnal communication) and Griffithsia okiensis (1,104 ESTs, Lee et al. 2007), and cDNA micro- or
macroarrays have been used to monitor gene expression in both Chondrus crispus (Collén et al. 2006a) and Porphyra yezoensis (Kitade et al. 2008). However,
currently the only complete red algal genome sequence available is that of
C. merolae, a unicellular organism from hot acid springs that has a highly reduced
and unusual genome. A second project is in progress, for Galdieria sulphuraria,
(http://genomics.msu.edu/galdieria/about.html) but this is also a non-marine, unicellular, extremophile red alga. Both of these organisms have very small, highly
derived genomes, which are of limited relevance to understanding many red algal
features. A genome sequence for a more “typical” red alga would be extremely
useful both to further our understanding of red algal biology and as a reference
for tracing the origins of genes acquired via endosymbiotic events. In response to
this need, genome projects have recently been initiated for two red macroalgae,
the florideophyte Chondrus crispus (at Genoscope, France) and the bangiophyte
Porphyra umbilicalis (at the Joint Genome Institute, USA).
These two genome projects are likely to be highly compatible. Both seaweeds
are ecologically important in specific habitats. They can both be handled relatively
easily in the laboratory and each has been the subject of extensive laboratory studies. Porphyra spp. are perhaps the best adapted to laboratory work, previous studies
have reported the isolation of mutant strains (Ohme and Miura 1988, Mitman and
van der Meer 1994, Yan et al. 2000), identification of genetic markers (Park et al.
2007), the preparation and regeneration of protoplasts (Waaland et al. 1990), whole
mount in situ hybridisation (Shimizu et al. 2004) and progress towards the development of genetic transformation (Cheney et al. 2001, He et al. 2001, Lin et al.
2001). Indeed, a related species, Porphyra yezoensis, has been proposed as a candidate model macroalgae (Kitade et al. 2004, Waaland et al. 2004). C. crispus has
the advantage of possessing a smaller genome (150 Mbp, Peters et al. 2004) than