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F. Raible and P.R.H. Steinmetz
even contribute to speciation itself. Comparison of alternative splice variants over
larger evolutionary time scales has so far been limited by the restricted coverage of
splice variants in given model systems (Boue et al. 2003, Brett et al. 2002), and
cases such as the aforementioned isoform diversity of Dscam in pancrustaceans
rather seem to point towards mainly independent expansion of splice variants in
different lineages. As the issue of coverage might soon be less relevant due to the
technological progress in high-throughput sequencing, it will be interesting to see
if there are systematic differences in the extent of alternative splicing in species of
different organizational level.
5.11 Sea Urchins: Unexpected Functional Repertoires
at the Base of Deuterostomes
Sea urchins are among the oldest experimental model systems used by marine biologists. In the second half of the twentieth century, experimental approaches have
been taken to the biochemical and molecular levels, with seminal work focusing
on the elucidation of transcriptional regulatory networks. The purple sea urchin,
Strongylocentrotus purpuratus, has thereby become a major model system for the
analysis of developmental gene-regulatory networks. The recent sequencing of
the Strongylocentrotus genome (Sea Urchin Genome Sequencing et al. 2006) has
boosted experimental research in the urchin, and also provided first insights into an
echinoderm genome. Three aspects are of particular relevance in the context of this
chapter: first, the sea urchin genome draft displayed an unprecedented number of
genes that – judged by their domain composition – are likely to be associated with
innate immunity, including 222 Toll-like receptors, more than 20 times the number
found in the human genome (Hibino et al. 2006, Rast et al. 2006). Although direct
functional assays have not yet been performed on these receptors, the numbers suggest that the family has undergone dramatic secondary expansion in the evolutionary
lineage leading to sea urchins. Similarly, the sea urchin genome contains hundreds
of fast-evolving G-protein coupled receptors (GPCRs) that, based on their mode of
organisation and their expression patterns, are likely to be chemosensory receptors
(Raible et al. 2006). By analogy to the immune-related genes, the dramatic expansion of the sensory GPCR family contradicts the old notion that the sea urchin would
only possess a rudimentary sensory repertoire.
A third, fundamental aspect about the sea urchin genome is that it encodes
both a bilaterally symmetric larval form and a fundamentally different structure,
the radially symmetric postembryonic body whose cells replace most of the larval
structures. Hence, the programs of two different body plans are encoded in the same
genome. How this is achieved, is still not properly understood, as few studies have
attempted to analyse the activity of genes in postembryonic development. What has
been revealed by transcriptome profiling studies, however, is that nearly 80% of the
transcription factors encoded in the sea urchin genome are already active during
embryogenesis (Howard-Ashby et al. 2006), as are a similar proportion of genes
F. Raible and P.R.H. Steinmetz
even contribute to speciation itself. Comparison of alternative splice variants over
larger evolutionary time scales has so far been limited by the restricted coverage of
splice variants in given model systems (Boue et al. 2003, Brett et al. 2002), and
cases such as the aforementioned isoform diversity of Dscam in pancrustaceans
rather seem to point towards mainly independent expansion of splice variants in
different lineages. As the issue of coverage might soon be less relevant due to the
technological progress in high-throughput sequencing, it will be interesting to see
if there are systematic differences in the extent of alternative splicing in species of
different organizational level.
5.11 Sea Urchins: Unexpected Functional Repertoires
at the Base of Deuterostomes
Sea urchins are among the oldest experimental model systems used by marine biologists. In the second half of the twentieth century, experimental approaches have
been taken to the biochemical and molecular levels, with seminal work focusing
on the elucidation of transcriptional regulatory networks. The purple sea urchin,
Strongylocentrotus purpuratus, has thereby become a major model system for the
analysis of developmental gene-regulatory networks. The recent sequencing of
the Strongylocentrotus genome (Sea Urchin Genome Sequencing et al. 2006) has
boosted experimental research in the urchin, and also provided first insights into an
echinoderm genome. Three aspects are of particular relevance in the context of this
chapter: first, the sea urchin genome draft displayed an unprecedented number of
genes that – judged by their domain composition – are likely to be associated with
innate immunity, including 222 Toll-like receptors, more than 20 times the number
found in the human genome (Hibino et al. 2006, Rast et al. 2006). Although direct
functional assays have not yet been performed on these receptors, the numbers suggest that the family has undergone dramatic secondary expansion in the evolutionary
lineage leading to sea urchins. Similarly, the sea urchin genome contains hundreds
of fast-evolving G-protein coupled receptors (GPCRs) that, based on their mode of
organisation and their expression patterns, are likely to be chemosensory receptors
(Raible et al. 2006). By analogy to the immune-related genes, the dramatic expansion of the sensory GPCR family contradicts the old notion that the sea urchin would
only possess a rudimentary sensory repertoire.
A third, fundamental aspect about the sea urchin genome is that it encodes
both a bilaterally symmetric larval form and a fundamentally different structure,
the radially symmetric postembryonic body whose cells replace most of the larval
structures. Hence, the programs of two different body plans are encoded in the same
genome. How this is achieved, is still not properly understood, as few studies have
attempted to analyse the activity of genes in postembryonic development. What has
been revealed by transcriptome profiling studies, however, is that nearly 80% of the
transcription factors encoded in the sea urchin genome are already active during
embryogenesis (Howard-Ashby et al. 2006), as are a similar proportion of genes