Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists advocate genomic sequencing of ’living fossil’

15.11.2004


A team of Stanford University researchers led by Richard Myers, Ph.D., in collaboration with Chris Amemiya, Ph.D., of the Benaroya Research Institute in Seattle, campaign in the December issue of Genome Research for deciphering the genetic code of a "living fossil" fish, the coelacanth.



The genomic sequence of this large "hollow-spined" fish, which populates deep-sea volcanic caves, could hold valuable clues for biologists studying the evolution of vertebrate species. Coelacanths were believed to have been extinct until a live specimen was discovered in 1938 off the coast of South Africa. Both of the known coelacanth species that survive today, Latimeria chalumnae and Latimeria menadoensis, are anatomically similar to their fossil relatives. Furthermore, coelacanths have exhibited little morphological change since their emergence during the Devonian period approximately 360 million years ago.

To date, complete genomic sequences for more than 200 organisms have been obtained, and hundreds more are currently in progress (www.genomesonline.org). These efforts will enable scientists to perform detailed comparisons of the complete genetic codes from multiple species, identifying the sequence changes that contributed to evolutionary adaptation and speciation. Although a wide assortment of species have been chosen for sequencing, ranging from lampreys to armadillos (www.genome.gov/12511858), Myers observed: "We’re missing an organism that could really shed light on the emergence of land vertebrates. We don’t know what genomic changes accompanied the transition from water to land, and a coelacanth genome could help identify those events."


The coelacanth is one of only two living taxa to occupy the critical, highly informative phylogenetic position between ray-finned fishes and tetrapods. Fleshy, lobed fins, which are one of the defining characteristics of coelacanths, are thought to represent an intermediate evolutionary stage in the transformation of fins to limbs. Lobe-finned relatives of the coelacanth underwent morphological alterations that enabled them to emerge from the sea and inhabit terrestrial environments. Both the coelacanth and the lungfish – the only two living lobe-finned fishes – are related to important evolutionary progenitors of land vertebrates. However, the lungfish genome is very large (more than 100 billion nucleotides in length), making it technically impractical to sequence with currently available technology. The coelacanth genome, on the other hand, is estimated to be smaller than that of human or mouse, making it feasible for whole-genome sequencing.

Jim Noonan, Ph.D., a former graduate student on Myers’ team who carried out much of the work described in the Genome Research article, focused on a small but highly informative genomic segment from the Indonesian coelacanth (Latimeria menadoensis) called the protocadherin gene cluster. Encoding for proteins involved in the development and maturation of neurons and synapses in the brain, protocadherin clusters are not present in invertebrates, such as fruit fly (Drosophila melanogaster) or roundworm (Caenorhabditis elegans), but they are found in more evolutionarily complex species, including all vertebrates. Protocadherin gene clusters are composed of a tandem array of multiple gene copies, making them particularly prone to aberrant recombination and thus, to duplication and homogenization. Because this region appears so vulnerable to evolutionary change, Noonan, Amemiya and Myers predicted that the sequence of the coelacanth protocadherin cluster would be a good indicator of the utility of the whole coelacanth genome sequence for inferring vertebrate phylogeny.

Jane Grimwood, Jeremy Schmutz and Mark Dickson at the Stanford Human Genome Center generated more than 600,000 nucleotides of coelacanth genomic sequence spanning the protocadherin gene cluster. Using this sequence, Noonan determined that the structure of the coelacanth cluster was very similar to the orthologous human cluster. The coelacanth genome has 49 protocadherin cluster genes organized into the same three subclusters (alpha, beta, and gamma) as the 54 protocadherin cluster genes in human. In contrast, the zebrafish (Danio rerio) genome contains at least 97 protocadherin genes organized into two distinct clusters, resulting from a whole-genome duplication event.

A major discovery stemming from this work is that the coelacanth genome appears to be evolving slowly relative to land vertebrates and the teleost fishes. This makes the coelacanth genome a better reference for comparative sequence analyses involving land vertebrates than teleost genomes, which are commonly used for such studies but are highly derived due to a whole-genome duplication event. For these reasons, Myers and colleagues argue that the complete genomic sequence of the coelacanth would be valuable for identifying important genome modifications that occurred during the evolution of tetrapod species.

Maria A. Smit | EurekAlert!
Further information:
http://www.cshl.edu

More articles from Life Sciences:

nachricht Researchers identify potentially druggable mutant p53 proteins that promote cancer growth
09.12.2016 | Cold Spring Harbor Laboratory

nachricht Plant-based substance boosts eyelash growth
09.12.2016 | Fraunhofer-Institut für Angewandte Polymerforschung IAP

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Electron highway inside crystal

Physicists of the University of Würzburg have made an astonishing discovery in a specific type of topological insulators. The effect is due to the structure of the materials used. The researchers have now published their work in the journal Science.

Topological insulators are currently the hot topic in physics according to the newspaper Neue Zürcher Zeitung. Only a few weeks ago, their importance was...

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Researchers identify potentially druggable mutant p53 proteins that promote cancer growth

09.12.2016 | Life Sciences

Scientists produce a new roadmap for guiding development & conservation in the Amazon

09.12.2016 | Ecology, The Environment and Conservation

Satellites, airport visibility readings shed light on troops' exposure to air pollution

09.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>