Thursday, December 28, 2006
From the journal Developmental Biology: Free online access to Volume 300 Issue 1, Sea Urchin Genome: Implications and Highlights up until end of June for non-subscribers.
From Eric Davidson's* introductory paper "Special issue: The sea urchin genome":
The 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-related 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...
...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 pre-genomic 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 non-chordate marine genome to be sequenced, the first sequence of a maximum indirectly developing animal, as well as the first echinoderm genome...
1) Shedding genomic light on Aristotle's lantern
Erica Sodergren, Yufeng Shen, Xingzhi Song, Lan Zhang, Richard A. Gibbs, George M. Weinstock
Sea urchins have proved fascinating to biologists since the time of Aristotle who compared the appearance of their bony mouth structure to a lantern in The History of Animals. Throughout modern times it has been a model system for research in developmental biology. Now, the genome of the sea urchin Strongylocentrotus purpuratus is the first echinoderm genome to be sequenced. A high quality draft sequence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with sequences from a collection of BACs selected to form a minimal tiling path along the genome. A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. This was overcome by use of the BAC tiling path backbone, in which each BAC represents a single haplotype, as well as by improvements in the Atlas software. Another innovation introduced in this project was the sequencing of pools of tiling path BACs rather than individual BAC sequencing. The Clone-Array Pooled Shotgun Strategy greatly reduced the cost and time devoted to preparing shotgun libraries from BAC clones. The genome sequence was analyzed with several gene prediction methods to produce a comprehensive gene list that was then manually refined and annotated by a volunteer team of sea urchin experts. This latter annotation community edited over 9000 gene models and uncovered many unexpected aspects of the sea urchin genetic content impacting transcriptional regulation, immunology, sensory perception, and an organism's development. Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development.
2) High regulatory gene use in sea urchin embryogenesis: Implications for
bilaterian development and evolution
Meredith Howard-Ashby, Stefan C. Materna, C. Titus Brown, Qiang Tu, Paola Oliveri,
R. Andrew Cameron, Eric H. Davidson
A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total “regulome” of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity.
*From Eric Davidson's lab homepage:
"...The major focus of research in our laboratory is on gene networks that control development and their evolution. Our areas of research include the transcriptional mechanisms by which specification of embryonic blastomeres occurs early in development; structure/function relationships in developmental cis-regulatory systems; sea urchin genomics; and regulatory evolution in the bilaterians. Most of our work is carried out on sea urchin embryos, which provide key experimental advantages..."
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