220
M.L. Cancela et al.
Zhikong Scallop (Chlamys farreri) and their use to identify genes involved in the
innate immune system of molluscs. A 10X genome coverage BAC library of the
Pacific oyster has been recently produced and fingerprinted as part of a project
coordinated by P. Gaffney (University of Delaware, USA).
7.2.4 High Quality Draft Genome Sequences
To date, the genomes of five teleost species, D. rerio, T. nigroviridis, O. latipes,
T. rubripes, and G. aculeatus, have been sequenced at high coverage. The
most recent sequence assemblies for all these genome sequences are available at www.ensembl.org. Two of these species, T. rubripes (fugu) and
G. aculeatus (stickleback), are marine fish, although only the former is fully marine
while the latter shows a freshwater and a marine morphotype, returning in some
cases to freshwater to breed. Sequence coverage of these two fish genomes is only
slightly different, 8.7X for T. rubripes and 11X for G. aculeatus. Nevertheless, a
comparison between the two species presents an interesting example of how information content of genome sequences might vary. The fugu genome is 393 Mb in size
and is represented by 7,213 scaffolds, with the largest scaffold being 7 Mb in size.
On the other hand, the stickleback genome is larger (approximately 460 Mb), but
the assembly shows 21 chromosomes (groups) with an additional 1,822 unplaced
supercontigs. It is quite obvious that the stickleback genome offers the means for
a better and more meaningful comparison with other fish genomes. In fact, both
linkage and RH maps of different fish species have been anchored against the stickleback genome (Franch et al. 2006, Sarropoulou et al. 2007, 2008, Bouza et al. 2007;
Fig. 7.2), showing a remarkable level of synteny, with the majority of genomic
rearrangements occurring at the intra-chromosomal level. As already mentioned,
novel DNA sequencing technologies will likely make it possible to undertake wholegenome sequencing projects in non-model species, however supporting tools such
as linkage and physical maps will be still necessary for high quality assembly of
these genomes. This approach is currently being developed for the Pacific oyster as
a joined effort beween P. R. China (Institute of Oceanology of Chinese Academy of
Sciences and Beijing Genomics Institute) and members of the international Oyster
Genome Consortium. Following the sequence of the limpet Lottia gigantea (see JGI
website), the oyster will be among the first members of the Lophotrochozoa to be
fully sequenced.
7.2.5 Functional Genomic Tools
In the genomic area, one principle focus is to translate information obtained using
large scale sequencing projects into enhanced understanding of genome function related to biological mechanisms and phenotypic variability. From the set
of EST collections usually incorporated into a publicly available database where
M.L. Cancela et al.
Zhikong Scallop (Chlamys farreri) and their use to identify genes involved in the
innate immune system of molluscs. A 10X genome coverage BAC library of the
Pacific oyster has been recently produced and fingerprinted as part of a project
coordinated by P. Gaffney (University of Delaware, USA).
7.2.4 High Quality Draft Genome Sequences
To date, the genomes of five teleost species, D. rerio, T. nigroviridis, O. latipes,
T. rubripes, and G. aculeatus, have been sequenced at high coverage. The
most recent sequence assemblies for all these genome sequences are available at www.ensembl.org. Two of these species, T. rubripes (fugu) and
G. aculeatus (stickleback), are marine fish, although only the former is fully marine
while the latter shows a freshwater and a marine morphotype, returning in some
cases to freshwater to breed. Sequence coverage of these two fish genomes is only
slightly different, 8.7X for T. rubripes and 11X for G. aculeatus. Nevertheless, a
comparison between the two species presents an interesting example of how information content of genome sequences might vary. The fugu genome is 393 Mb in size
and is represented by 7,213 scaffolds, with the largest scaffold being 7 Mb in size.
On the other hand, the stickleback genome is larger (approximately 460 Mb), but
the assembly shows 21 chromosomes (groups) with an additional 1,822 unplaced
supercontigs. It is quite obvious that the stickleback genome offers the means for
a better and more meaningful comparison with other fish genomes. In fact, both
linkage and RH maps of different fish species have been anchored against the stickleback genome (Franch et al. 2006, Sarropoulou et al. 2007, 2008, Bouza et al. 2007;
Fig. 7.2), showing a remarkable level of synteny, with the majority of genomic
rearrangements occurring at the intra-chromosomal level. As already mentioned,
novel DNA sequencing technologies will likely make it possible to undertake wholegenome sequencing projects in non-model species, however supporting tools such
as linkage and physical maps will be still necessary for high quality assembly of
these genomes. This approach is currently being developed for the Pacific oyster as
a joined effort beween P. R. China (Institute of Oceanology of Chinese Academy of
Sciences and Beijing Genomics Institute) and members of the international Oyster
Genome Consortium. Following the sequence of the limpet Lottia gigantea (see JGI
website), the oyster will be among the first members of the Lophotrochozoa to be
fully sequenced.
7.2.5 Functional Genomic Tools
In the genomic area, one principle focus is to translate information obtained using
large scale sequencing projects into enhanced understanding of genome function related to biological mechanisms and phenotypic variability. From the set
of EST collections usually incorporated into a publicly available database where