Decoded Sea Urchin Genome Shows Surprising Relationship To Humans

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Decoded Sea Urchin Genome Shows Surprising Relationship To Humans

http://www.sciencedaily.com/releases/2006/11/061109153835.htm

The Sea Urchin Genome Sequencing Project (SUGSP) Consortium, led by

the Human Genome Sequencing Center at Baylor College of Medicine

(BCM-HGSC) in Houston, announced today the decoding and analysis of

the genome sequence of the sea urchin, Strongylocentrotus purpuratus.

The results are presented in the Nov. 10 issue of the journal

Science, and 41 companion manuscripts describing further detailed

analyses are contained in that journal and in a special issue of the

journal Developmental Biology, appearing on Dec.1, 2006.

The genome of a male California purple sea urchin was sequenced,

which contained more than 814 million DNA " letters, " spelling out

23,300 genes. Nearly 10,000 of the genes were scrutinized by an

international consortium of 240 scientists from more than 70

institutions in 11 countries. The sequence covers more than 90

percent of the genome.

The BCM-HGSC generated the sequence data for the SUGSP, then

assembled the genome and led the analysis consortium. Additional

resources for the project included a BAC library (clones with very

large pieces of DNA) prepared at the California Institute of

Technology and a physical map prepared at the Genome

Sciences Centre at the British Columbia Cancer Agency in Vancouver.

The project was led by a Sodergren and Weinstock, a team

at the BCM-HGSC, along with Gibbs, director of the BCM-HGSC,

and son and Cameron of the California Institute of

Technology. The National Human Genome Research Institute of the

National Institutes of Health provided funding for the SUGSP, with

the National Science Foundation (NSF) also a supporter.

" Unraveling the sea urchin genome has yielded striking similarities

and surprising differences between sea urchins and humans, " said

Judith Venuti, program director in NSF's Integrative Organismal

Biology Division.

" Expansion of sequencing beyond medically-relevant organisms is

providing scientists with a treasure trove of new insights and

information, " added Judith Plesset, also a program director in NSF's

Integrative Organismal Biology Division.

Sea urchins are echinoderms (Greek for spiny skin), marine animals

that originated over 540 million years ago and include starfish,

brittle stars, sea lilies, and sea cucumbers. Following the great

extinction of animals 250 million years ago, the modern sea urchins

emerged as dominant echinoderm species. The purple sea urchin

emerged in the North Pacific Ocean during a rapid burst of

speciation and diversification 15-20 million years ago.

There was great interest in the sea urchin as a target for genome

sequencing because these animals share a common ancestor with

humans, scientists said. That ancestor lived over 540 million years

ago and gave rise to the Deuterostomes, the super phylum of animals

that includes phyla such as echinoderms and chordates, the phylum to

which humans and other vertebrates belong.

All Deuterostomes are more closely related to each other than they

are to any other animals not included in the Deuterostome super

phylum. For example, among sequenced genomes, the genomes of fruit

flies and worms are more distant from the sea urchin genome than is

the human genome.

" This analysis shows that sea urchins share substantially more genes

and biological pathways with humans than previously suspected, " said

Francis , director of the National Human Genome Research

Institute at the National Institutes of Health, which supported the

research. " Comparing the genome of the sea urchin with that of the

human and other model organisms will provide scientists with novel

insights into the structure and function of our own genome. "

To discover how sea urchins and humans can be so different, yet be

related by descent from an ancient relative, their genomes were

compared. The sea urchin is an invertebrate and the first example of

a Deuterostome genome outside the chordates.

The sea urchin fills a large evolutionary gap in sequenced genomes, "

said Weinstock. " It allows us to see what went on in evolution after

the split between the ancestors that gave rise to humans and

insects. The sea urchin genome provided plenty of unexpected rewards

and was a great choice for sequencing. "

Comparing the genes of the sea urchin to the human gene list shows

which human genes are likely to be recent innovations in human

evolution and which are ancient. It also shows which human genes

have changed slowly in the lineage from the ancestral Deuterostome

animal and which are evolving rapidly in response to natural

selection.

This information, scientists say, will make it possible one day to

know the history of every human gene - and build a picture of what

the extinct ancestors that gave rise to animal life from worms to

humans looked like.

" More than 30 years ago Roy Britten and son offered a

comprehensive theory of gene regulation in higher organisms and the

sea urchin has been the premier model for testing these predictions "

said Gibbs, Director of the BCM-HGSC. " The complete sequence

is now available to further these studies. "

Because of its evolutionary position, the sea urchin genome sequence

was unknown biological territory, said scientists affiliated with

the SUGSP.

Some of their discoveries are:

The sea urchin had most of the same gene families found in humans,

the Deuterostome toolkit used to create animals in this super

phylum. However the size of gene families was often larger in

humans, reflecting in part two whole genome duplication events

during vertebrate evolution, after the separation of the sea urchin

and human evolutionary lines.

One unexpected exception to this size rule was the immune system.

Humans have innate and acquired immunity systems. The sea urchin has

some of the genes of the acquired immunity system, but its innate

immunity branch is greatly expanded with 10 to 20 times as many

genes as in humans. Innate immunity is the set of proteins that

are " hard-wired " to detect unique molecules of bacteria, such as

their cell walls, and signal alert the body to the intruders.

The sea urchin has genes for sensory proteins that are involved in

vision and hearing in man. Yet the sea urchin has no eyes or ears,

at least as we know them. Some of the visual sensory proteins are

located to an appendage known as the tube foot, and likely function

in sensory processes there. It is remarkable that the same sensory

proteins are used in organs with such different structures in sea

urchins and man, said Sodergren.

" The sea urchin reminds us of the underlying unity of all life on

earth, " she said. " It is a similar set of genes and proteins being

reused in different ways, different numbers, and at different times

in the life cycle to create the diversity of living forms. "

The sequencing for this project was supported by NIH. The analysis

and annotation were largely supported by NSF.