7 Genomic Approaches in Aquaculture and Fisheries
221
they are assembled into contigs, subsequent microarray design or assignment of
SAGE (Serial Analysis of Gene Expression) or MPSS (Massively Parallel Signature
Sequencing) signatures allow transcriptome profiling to be carried out to study
marine animal physiology. Functional genomics focuses on dynamic aspects of the
genome such as gene transcription, translation, and protein–protein interactions. We
will refer here to functional genomics in a restricted way, i.e. transcriptomics. The
analysis of a whole-genome transcriptome in a single experiment has become feasible with the introduction of the DNA microarray technology (Schena et al. 1995).
Eukaryotic cell transcriptomes proved to be much more complex than thought and
thus difficult to represent fully in a single experiment (Birney et al. 2007), but DNA
microarrays have indeed given a totally new perspective to gene expression studies.
There are several technical options for the construction of gene-expression DNA
microarray, e.g. probes might be either spotted cDNAs or oligos, or oligos of various lengths can be synthesized in situ using several different synthesis technologies
(Holloway et al. 2002). Until recently the array platforms available for marine fish
and shellfish species were spotted cDNA microarrays. The alternative approach is
now represented by oligonucleotide probes, designed on all in silico available cDNA
sequences, which are then synthesized and spotted or directly synthesized on the
glass slide.
For two oyster species, C. virginica and C. gigas, an international group of collaborators has constructed a cDNA microarray (4,460 sequences from C. virginica
and 2,320 from C. gigas) (Jenny et al. 2007). This array is notably used to estimate the response of C. gigas families to heat stress challenge (Lang et al. 2008). In
Europe, within the framework of Marine Genomics Europe network of excellence
and the Aquafirst European project, a larger portion of the Pacific oyster transcriptome was spotted to produce a 10X microarray slide. This slide was used to examine
the biological mechanisms involved in the response of lines selected to be resistant
or sensitive to summer mortality (Boudry et al. 2008; E Fleury, personal communication). In the blue mussel, a species commonly used as a sentinel to monitor
pollution in the marine environment, a first cDNA microarray was designed including 1,714 probes allowing the identification of about 50 signatures of relevant doses
of pollutants in mussel tissues (Venier et al. 2006). A low-density oligonucleotide
microarray, representing 24 mussel genes selected on the basis of their potential
involvement in mechanisms of pollutants and xenobiotic response, was also validated (Dondero et al. 2006). Finally, from microarray data obtained in the intertidal
mussel Mytilus californiacus across major portions of its biogeographical range,
Place et al. (2008) emphasised the usefulness of such transcriptomic tools to marine
ecologists for ecological studies including those relevant to the marine estuarine
habitat of the bivalves.
The expanding number of EST available in public data bases for many marine
species (e.g. Salmo salar 433,337, G. aculeatus 276,992, Gadus morhua 181,734,
D. labrax 32,755 and C. gigas 56,327) have paved the way for a much broader
use of oligo-DNA microarrays. Within the European Network of Excellence
“Marine Genomics Europe”, a pilot study aid at developing such platform for
two marine fish (S. aurata and D. labrax) has been carried out. Using an in
221
they are assembled into contigs, subsequent microarray design or assignment of
SAGE (Serial Analysis of Gene Expression) or MPSS (Massively Parallel Signature
Sequencing) signatures allow transcriptome profiling to be carried out to study
marine animal physiology. Functional genomics focuses on dynamic aspects of the
genome such as gene transcription, translation, and protein–protein interactions. We
will refer here to functional genomics in a restricted way, i.e. transcriptomics. The
analysis of a whole-genome transcriptome in a single experiment has become feasible with the introduction of the DNA microarray technology (Schena et al. 1995).
Eukaryotic cell transcriptomes proved to be much more complex than thought and
thus difficult to represent fully in a single experiment (Birney et al. 2007), but DNA
microarrays have indeed given a totally new perspective to gene expression studies.
There are several technical options for the construction of gene-expression DNA
microarray, e.g. probes might be either spotted cDNAs or oligos, or oligos of various lengths can be synthesized in situ using several different synthesis technologies
(Holloway et al. 2002). Until recently the array platforms available for marine fish
and shellfish species were spotted cDNA microarrays. The alternative approach is
now represented by oligonucleotide probes, designed on all in silico available cDNA
sequences, which are then synthesized and spotted or directly synthesized on the
glass slide.
For two oyster species, C. virginica and C. gigas, an international group of collaborators has constructed a cDNA microarray (4,460 sequences from C. virginica
and 2,320 from C. gigas) (Jenny et al. 2007). This array is notably used to estimate the response of C. gigas families to heat stress challenge (Lang et al. 2008). In
Europe, within the framework of Marine Genomics Europe network of excellence
and the Aquafirst European project, a larger portion of the Pacific oyster transcriptome was spotted to produce a 10X microarray slide. This slide was used to examine
the biological mechanisms involved in the response of lines selected to be resistant
or sensitive to summer mortality (Boudry et al. 2008; E Fleury, personal communication). In the blue mussel, a species commonly used as a sentinel to monitor
pollution in the marine environment, a first cDNA microarray was designed including 1,714 probes allowing the identification of about 50 signatures of relevant doses
of pollutants in mussel tissues (Venier et al. 2006). A low-density oligonucleotide
microarray, representing 24 mussel genes selected on the basis of their potential
involvement in mechanisms of pollutants and xenobiotic response, was also validated (Dondero et al. 2006). Finally, from microarray data obtained in the intertidal
mussel Mytilus californiacus across major portions of its biogeographical range,
Place et al. (2008) emphasised the usefulness of such transcriptomic tools to marine
ecologists for ecological studies including those relevant to the marine estuarine
habitat of the bivalves.
The expanding number of EST available in public data bases for many marine
species (e.g. Salmo salar 433,337, G. aculeatus 276,992, Gadus morhua 181,734,
D. labrax 32,755 and C. gigas 56,327) have paved the way for a much broader
use of oligo-DNA microarrays. Within the European Network of Excellence
“Marine Genomics Europe”, a pilot study aid at developing such platform for
two marine fish (S. aurata and D. labrax) has been carried out. Using an in