204
S.M. Coelho et al.
Genomic approaches have only just started to be applied to marine algal ecosystems. The handful of genome sequences that are available for planktonic microalgae,
for example, have provided important insights into how these organisms function in
their environment but these studies have only scratched the surface of the complexity of these ecosystems. Future studies will combine environmental sequencing data
with genome information for individual strains to provide a better understanding
both of the biodiversity present and of the characteristics of component species.
These approaches will be combined with methods that allow the analysis of gene
expression such as cDNA sequencing or microarray analysis providing, not only a
census of the genes present in an ecosystem but also an overview of which genes
are active under particular conditions. Similar studies are planned for macroalgae in
coastal environments. The larger size of macroalgal genomes limits the number of
genome sequencing projects at present but the rapid progress that is being made with
these technologies is expected to modify this situation in the coming years. Together
these future studies are expected to provide more detailed descriptions of the roles
of algae in marine biosytems, particularly in terms of their key influence on biogeochemical cycles and their responses to climate change and other anthropogenic
impacts.
One of the consequences of the broad phylogenetic distribution of the algae
across several very ancient eukaryotic groups is that they represent an enormous
potential for the discovery of novel biological processes including metabolic pathways, signalling pathways, cellular processes, developmental regulation, etc. One
of the surprising results of algal sequencing projects has often been the very high
proportion of genes that have no matches in the public databases. For example,
this was the case for about half the genes in the genome of the diatom T. pseudonana (Armbrust et al. 2004). A major challenge for the future will be to understand
the cellular functions of these “orphan” genes and the development of a number of
model organisms for both the micro and the macroalgae is an important step towards
this objective.
References
Allen AE, Vardi A, Bowler C (2006) An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr Opin Plant Biol 9:
264–273
Archibald JM (2007) Nucleomorph genomes: structure, function, origin and evolution. Bioessays
29:392–402
Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.
Proc Natl Acad Sci U S A 100:7678–7683
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt
KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC,
Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov
VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant
A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA,
Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The
S.M. Coelho et al.
Genomic approaches have only just started to be applied to marine algal ecosystems. The handful of genome sequences that are available for planktonic microalgae,
for example, have provided important insights into how these organisms function in
their environment but these studies have only scratched the surface of the complexity of these ecosystems. Future studies will combine environmental sequencing data
with genome information for individual strains to provide a better understanding
both of the biodiversity present and of the characteristics of component species.
These approaches will be combined with methods that allow the analysis of gene
expression such as cDNA sequencing or microarray analysis providing, not only a
census of the genes present in an ecosystem but also an overview of which genes
are active under particular conditions. Similar studies are planned for macroalgae in
coastal environments. The larger size of macroalgal genomes limits the number of
genome sequencing projects at present but the rapid progress that is being made with
these technologies is expected to modify this situation in the coming years. Together
these future studies are expected to provide more detailed descriptions of the roles
of algae in marine biosytems, particularly in terms of their key influence on biogeochemical cycles and their responses to climate change and other anthropogenic
impacts.
One of the consequences of the broad phylogenetic distribution of the algae
across several very ancient eukaryotic groups is that they represent an enormous
potential for the discovery of novel biological processes including metabolic pathways, signalling pathways, cellular processes, developmental regulation, etc. One
of the surprising results of algal sequencing projects has often been the very high
proportion of genes that have no matches in the public databases. For example,
this was the case for about half the genes in the genome of the diatom T. pseudonana (Armbrust et al. 2004). A major challenge for the future will be to understand
the cellular functions of these “orphan” genes and the development of a number of
model organisms for both the micro and the macroalgae is an important step towards
this objective.
References
Allen AE, Vardi A, Bowler C (2006) An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr Opin Plant Biol 9:
264–273
Archibald JM (2007) Nucleomorph genomes: structure, function, origin and evolution. Bioessays
29:392–402
Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.
Proc Natl Acad Sci U S A 100:7678–7683
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt
KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC,
Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov
VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant
A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA,
Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The