6 Genomics of Marine Algae
201
under laboratory conditions, its high fertility and rapid growth (the life cycle can
be completed in 2 months) and the ease with which genetic crosses can be carried
out (Peters et al. 2004). The aim with this organism, therefore, has been to develop
it as a model system that will allow analyses to go beyond a simple inventory of
the genes present in the genome. Ectocarpus was selected because it presents the
possibility of using genetic approaches to analyse gene function.
Sequencing of the Ectocarpus genome was completed in 2007 and a number
of additional genomic tools are now available including whole genome tiling array
data and 91,000 cDNA sequences corresponding to several stages of the life cycle.
In terms of laboratory techniques, classical genetic approaches such as mutagenesis, screening for mutant lines, crosses and complementation analysis can be carried
out routinely. Several cell biology tools including in vivo and in vitro imaging,
microinjection and protoplast regeneration are also available. Additional tools currently under development include a genetic map, a genetic transformation protocol,
RNAi-based gene knockdowns and positional cloning of mutated loci.
With the above list of tools in hand, Ectocarpus is now being used as a model
to investigate a broad range of topics related to brown algal biology. Recent work
aimed at understanding how the life cycle is regulated provides a good example
(Coelho et al. 2007, Peters et al. 2008). Ectocarpus has a haploid-diploid life cycle
involving alternation between sporophyte and gametophyte generations (Müller
1967). In an effort to understand how the switch between the two generations is controlled, screens have been carried out for mutants in which this process is perturbed.
In one mutant, immediate upright (imm), the sporophyte is partially converted into a
gametophyte, exhibiting a pattern of early development that closely resembles that
of the gametophyte but, nonetheless, producing spores rather than gametes. Analysis
of gene expression in this mutant using microarray analysis and quantitative PCR,
showed that a large number of genes that are normally expressed during the gametophyte generation are expressed in the sporophyte of this mutant. Future work
involving the analysis of additional mutant lines, genome-scale analyses of changes
in gene regulation in these mutants and identification of mutated genes by positional
cloning is expected to provide further insights into the regulatory mechanisms that
control the life cycle in the coming years.
Similar approaches have been initiated in an effort to understand other aspects of
Ectocarpus biology including, for example, sex determination, morphogenesis, cell
wall biosynthesis and responses to biotic and abiotic stresses. Much of the information obtained will be of general relevance to the brown algae as a group, with
potential applications including the identification of novel biomolecules and the
exploitation of genetic data in future seaweed breeding programs.
6.4.6.2 Red Macroalgae
Red macroalgae are found in a wide range of shoreline habitats ranging from
the extreme high shore to the lower limit of the photic zone. Several species are
exploited for food and industrial applications. About 2.8 million tonnes of red algae
are harvested annually, with a value of approximately 2,000 million US dollars (FAO
201
under laboratory conditions, its high fertility and rapid growth (the life cycle can
be completed in 2 months) and the ease with which genetic crosses can be carried
out (Peters et al. 2004). The aim with this organism, therefore, has been to develop
it as a model system that will allow analyses to go beyond a simple inventory of
the genes present in the genome. Ectocarpus was selected because it presents the
possibility of using genetic approaches to analyse gene function.
Sequencing of the Ectocarpus genome was completed in 2007 and a number
of additional genomic tools are now available including whole genome tiling array
data and 91,000 cDNA sequences corresponding to several stages of the life cycle.
In terms of laboratory techniques, classical genetic approaches such as mutagenesis, screening for mutant lines, crosses and complementation analysis can be carried
out routinely. Several cell biology tools including in vivo and in vitro imaging,
microinjection and protoplast regeneration are also available. Additional tools currently under development include a genetic map, a genetic transformation protocol,
RNAi-based gene knockdowns and positional cloning of mutated loci.
With the above list of tools in hand, Ectocarpus is now being used as a model
to investigate a broad range of topics related to brown algal biology. Recent work
aimed at understanding how the life cycle is regulated provides a good example
(Coelho et al. 2007, Peters et al. 2008). Ectocarpus has a haploid-diploid life cycle
involving alternation between sporophyte and gametophyte generations (Müller
1967). In an effort to understand how the switch between the two generations is controlled, screens have been carried out for mutants in which this process is perturbed.
In one mutant, immediate upright (imm), the sporophyte is partially converted into a
gametophyte, exhibiting a pattern of early development that closely resembles that
of the gametophyte but, nonetheless, producing spores rather than gametes. Analysis
of gene expression in this mutant using microarray analysis and quantitative PCR,
showed that a large number of genes that are normally expressed during the gametophyte generation are expressed in the sporophyte of this mutant. Future work
involving the analysis of additional mutant lines, genome-scale analyses of changes
in gene regulation in these mutants and identification of mutated genes by positional
cloning is expected to provide further insights into the regulatory mechanisms that
control the life cycle in the coming years.
Similar approaches have been initiated in an effort to understand other aspects of
Ectocarpus biology including, for example, sex determination, morphogenesis, cell
wall biosynthesis and responses to biotic and abiotic stresses. Much of the information obtained will be of general relevance to the brown algae as a group, with
potential applications including the identification of novel biomolecules and the
exploitation of genetic data in future seaweed breeding programs.
6.4.6.2 Red Macroalgae
Red macroalgae are found in a wide range of shoreline habitats ranging from
the extreme high shore to the lower limit of the photic zone. Several species are
exploited for food and industrial applications. About 2.8 million tonnes of red algae
are harvested annually, with a value of approximately 2,000 million US dollars (FAO