Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Scientists advocate genomic sequencing of ’living fossil’


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 ( 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 (, 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:

More articles from Life Sciences:

nachricht Molecular doorstop could be key to new tuberculosis drugs
20.03.2018 | Rockefeller University

nachricht Modified biomaterials self-assemble on temperature cues
20.03.2018 | Duke University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Mars' oceans formed early, possibly aided by massive volcanic eruptions

Oceans formed before Tharsis and evolved together, shaping climate history of Mars

A new scenario seeking to explain how Mars' putative oceans came and went over the last 4 billion years implies that the oceans formed several hundred million...

Im Focus: Tiny implants for cells are functional in vivo

For the first time, an interdisciplinary team from the University of Basel has succeeded in integrating artificial organelles into the cells of live zebrafish embryos. This innovative approach using artificial organelles as cellular implants offers new potential in treating a range of diseases, as the authors report in an article published in Nature Communications.

In the cells of higher organisms, organelles such as the nucleus or mitochondria perform a range of complex functions necessary for life. In the networks of...

Im Focus: Locomotion control with photopigments

Researchers from Göttingen University discover additional function of opsins

Animal photoreceptors capture light with photopigments. Researchers from the University of Göttingen have now discovered that these photopigments fulfill an...

Im Focus: Surveying the Arctic: Tracking down carbon particles

Researchers embark on aerial campaign over Northeast Greenland

On 15 March, the AWI research aeroplane Polar 5 will depart for Greenland. Concentrating on the furthest northeast region of the island, an international team...

Im Focus: Unique Insights into the Antarctic Ice Shelf System

Data collected on ocean-ice interactions in the little-researched regions of the far south

The world’s second-largest ice shelf was the destination for a Polarstern expedition that ended in Punta Arenas, Chile on 14th March 2018. Oceanographers from...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

Virtual reality conference comes to Reutlingen

19.03.2018 | Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

International Tinnitus Conference of the Tinnitus Research Initiative in Regensburg

13.03.2018 | Event News

Latest News

Physicists made crystal lattice from polaritons

20.03.2018 | Physics and Astronomy

Mars' oceans formed early, possibly aided by massive volcanic eruptions

20.03.2018 | Physics and Astronomy

Thawing permafrost produces more methane than expected

20.03.2018 | Earth Sciences

Science & Research
Overview of more VideoLinks >>>