Special issue: The sea urchin genome

Developmental Biology 300 (2006) 1www.elsevier.com/locate/ydbio

Announcement

Special issue: The sea urchin genome

The Strongylocentrotus purpuratus Genome Project focusedthe attention of the sea urchin research community as nothinghad ever done before. Two numbers tell the story. The first is themore than 9700 genes annotated by volunteers from thisresearch community, guided by the energetic leadership of EricaSodergren and George Weinstock at the Baylor College ofMedicine Human Genome Sequencing Center, where thesequence was obtained and the annotation effort was organized.The second is the number of papers in this very issue, whichcontains 36 individual studies no one of which could or wouldhave existed absent the genome sequence. Together with themain announcement of the genome sequence in Science andfour additional genome-related papers published with it, over 40diverse works have been called into existence with the advent ofthis sequence. The genome sequence provides a digitaldefinition of the potentialities of the animal, and these papersshow how many different kinds of potentiality it illuminated.

This collection contains remarkable surprises, and some ofthe papers herein literally set up new fields of scientificenterprise: for example, we learn that the sea urchin isequipped with olfactory and visual receptors of unsuspectedvariety, and that its immune system is like none ever seenbefore; these discoveries now demand functional explanation.One underlying reason for the richness of intellectual returnsfrom the sea urchin genome project is the phylogenetic positionof sea urchins. Unlike the majority of animals whose genomesequences have recently come on line, sea urchins are verydifferent from any other animal for which we have genomesequence information. The S. purpuratus genome sequence isthe first non-chordate deuterostome genome sequence we have,and so now we can see what cell adhesion genes, whatcytoskeletal genes, what signaling genes, what regulatorygenes, what biomineralization genes, what fertilization,detoxification, histone, and gametogenesis genes they shareand do not share with chordate deuterostomes and animals ofother superphyla. From there emerges both an understanding ofthe deuterostome clade such as we have never had before andan understanding of echinoderms and the phyletic signature oftheir genetic repertoire. The deuterostomes were first imagineda century ago on the basis of comparative embryo anatomy,perhaps the greatest early success story of that field; theirreality as a clade was indicated by pre-genomic evidence such

doi:10.1016/j.ydbio.2006.10.036

as intron position in shared genes, then strongly supported byrRNA and protein molecular phylogeny. But now this super-phylum, our own, is defined by the sea urchin genome projectin terms of the sharing patterns of literally thousands of genes.The other side of the coin is the gene families that appeared orhave hugely expanded during echinoderm evolution, mostprominently the sensory receptor genes, immune genes ofseveral large families, and the biomineralization genes, whichare unlike any seen elsewhere. It is no wonder that there aredifferences and surprises: this is also the first non-chordatemarine genome to be sequenced, the first sequence of amaximum indirectly developing animal, as well as the firstechinoderm genome.

The sea urchin was a research model from the earliest days ofgenome-oriented research. It was in sea urchins that the natureof pronuclear fusion at fertilization was discovered in the 1880s,and in sea urchin embryos, about a century ago, that wasdemonstrated the necessity for embryogenesis of a completenuclear genome in every blastomere. In our time, moleculardevelopmental biology of sea urchin embryos is remarkablyadvanced in three general areas which feed directly offgenomics and which in return feed our understanding ofgenome function: cis-regulatory structure/function relation-ships; gene regulatory networks for embryonic development;and the genomic basis for morphogenetic events, which areparticularly well studied in this relatively simple embryo. Allthree areas intersect at the genome.

This issue of genome-related papers is in truth the output ofthe whole sea urchin community; the intersection between itsvarious and many interests and the genome has personallyabsorbed all of us this last year and more. Several peoplecontributed particularly to the assembly of this special issue ofDevelopmental Biology, in addition to the many authors, co-authors, and reviewers of the 36 papers within: Erica Sodergrenat HGSC worked closely with us in organizing this issue, as didJane Rigg at Caltech; Jill Ovren at Developmental Biology wasinvariably both helpful and decisive; and I personally wouldlike to thank Dave McClay and Richard Hynes, who servedwith me as co-editors of these papers.

Eric DavidsonE-mail address: [email protected].

mailto:YDBIO2917S0012-06)013301016/[email protected] Strongylocentrotus purpuratus Genome Project focused the attention of the sea urchin research community as nothing had ever done before. Two numbers tell the story. The first is the more than 9700 genes annotated by volunteers from this research community, guided by the energetic leadership of Erica Sodergren and George Weinstock at the Baylor College of Medicine Human Genome Sequencing Center, where the sequence was obtained and the annotation effort was organized. The second is the number of papers in this very issue, which contains 36 individual studies no one of which could or would have existed absent the genome sequence. Together with the main announcement of the genome sequence in Science and four additional genome-elated papers published with it, over 40 diverse works have been called into existence with the advent of this sequence. The genome sequence provides a digital definition of the potentialities of the animal, and these papers show how many different kinds of potentiality it illuminated.This collection contains remarkable surprises, and some of the papers herein literally set up new fields of scientific enterprise: for example, we learn that the sea urchin is equipped with olfactory and visual receptors of unsuspected variety, and that its immune system is like none ever seen before; these discoveries now demand functional explanation. One underlying reason for the richness of intellectual returns from the sea urchin genome project is the phylogenetic position of sea urchins. Unlike the majority of animals whose genome sequences have recently come on line, sea urchins are very different from any other animal for which we have genome sequence information. The S. purpuratus genome sequence is the first nonhordate deuterostome genome sequence we have, and so now we can see what cell adhesion genes, what cytoskeletal genes, what signaling genes, what regulatory genes, what biomineralization genes, what fertilization, detoxification, histone, and gametogenesis genes they share and do not share with chordate deuterostomes and animals of other superphyla. From there emerges both an understanding of the deuterostome clade such as we have never had before and an understanding of echinoderms and the phyletic signature of their genetic repertoire. The deuterostomes were first imagined a century ago on the basis of comparative embryo anatomy, perhaps the greatest early success story of that field; their reality as a clade was indicated by preenomic evidence such as intron position in shared genes, then strongly supported by rRNA and protein molecular phylogeny. But now this superphylum, our own, is defined by the sea urchin genome project in terms of the sharing patterns of literally thousands of genes. The other side of the coin is the gene families that appeared or have hugely expanded during echinoderm evolution, most prominently the sensory receptor genes, immune genes of several large families, and the biomineralization genes, which are unlike any seen elsewhere. It is no wonder that there are differences and surprises: this is also the first nonhordate marine genome to be sequenced, the first sequence of a maximum indirectly developing animal, as well as the first echinoderm genome.The sea urchin was a research model from the earliest days of genomeriented research. It was in sea urchins that the nature of pronuclear fusion at fertilization was discovered in the 1880s, and in sea urchin embryos, about a century ago, that was demonstrated the necessity for embryogenesis of a complete nuclear genome in every blastomere. In our time, molecular developmental biology of sea urchin embryos is remarkably advanced in three general areas which feed directly off genomics and which in return feed our understanding of genome function: cis-egulatory structure/function relationships; gene regulatory networks for embryonic development; and the genomic basis for morphogenetic events, which are particularly well studied in this relatively simple embryo. All three areas intersect at the genome.This issue of genome-elated papers is in truth the output of the whole sea urchin community; the intersection between its various and many interests and the genome has personally absorbed all of us this last year and more. Several people contributed particularly to the assembly of this special issue of Developmental Biology, in addition to the many authors, couthors, and reviewers of the 36 papers within: Erica Sodergren at HGSC worked closely with us in organizing this issue, as did Jane Rigg at Caltech; Jill Ovren at Developmental Biology was invariably both helpful and decisive; and I personally would like to thank Dave McClay and Richard Hynes, who served with me as coditors of these papers.

http://dx.doi.org/10.1016/j.ydbio.2006.10.036

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Special issue: The sea urchin genome